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Manganese in PDB 8f6m: Complex of Rabbit Muscle Pyruvate Kinase with Adp and the Phosphonate Analogue of Pep Mimicking the Michaelis Complex.

Enzymatic activity of Complex of Rabbit Muscle Pyruvate Kinase with Adp and the Phosphonate Analogue of Pep Mimicking the Michaelis Complex.

All present enzymatic activity of Complex of Rabbit Muscle Pyruvate Kinase with Adp and the Phosphonate Analogue of Pep Mimicking the Michaelis Complex.:
2.7.1.40; 2.7.10.2; 2.7.11.1;

Protein crystallography data

The structure of Complex of Rabbit Muscle Pyruvate Kinase with Adp and the Phosphonate Analogue of Pep Mimicking the Michaelis Complex., PDB code: 8f6m was solved by T.Holyoak, A.W.Fenton, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.02 / 2.15
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 93.026, 216.396, 258.151, 90, 90, 90
R / Rfree (%) 15.6 / 20.5

Other elements in 8f6m:

The structure of Complex of Rabbit Muscle Pyruvate Kinase with Adp and the Phosphonate Analogue of Pep Mimicking the Michaelis Complex. also contains other interesting chemical elements:

Potassium (K) 8 atoms

Manganese Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 15;

Binding sites:

The binding sites of Manganese atom in the Complex of Rabbit Muscle Pyruvate Kinase with Adp and the Phosphonate Analogue of Pep Mimicking the Michaelis Complex. (pdb code 8f6m). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 15 binding sites of Manganese where determined in the Complex of Rabbit Muscle Pyruvate Kinase with Adp and the Phosphonate Analogue of Pep Mimicking the Michaelis Complex., PDB code: 8f6m:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Manganese binding site 1 out of 15 in 8f6m

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Manganese binding site 1 out of 15 in the Complex of Rabbit Muscle Pyruvate Kinase with Adp and the Phosphonate Analogue of Pep Mimicking the Michaelis Complex.


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Complex of Rabbit Muscle Pyruvate Kinase with Adp and the Phosphonate Analogue of Pep Mimicking the Michaelis Complex. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn903

b:21.7
occ:1.00
 O1A A:ADP901 2.0 16.1 1.0
O A:HOH1060 2.1 21.5 1.0
O4 A:SIN902 2.1 26.4 1.0
O1B A:ADP901 2.1 18.2 1.0
O A:HOH1287 2.3 17.0 1.0
O3 A:SIN902 2.5 20.1 1.0
C4 A:SIN902 2.7 29.6 1.0
PB A:ADP901 3.3 18.0 1.0
PA A:ADP901 3.3 19.2 1.0
O3A A:ADP901 3.6 18.6 1.0
O3B A:ADP901 3.7 23.0 1.0
OD2 A:ASP177 4.0 24.7 1.0
O A:HOH1003 4.2 27.9 1.0
C3 A:SIN902 4.2 18.6 1.0
OG A:SER361 4.2 19.2 1.0
O2A A:ADP901 4.3 16.2 1.0
CB A:SER361 4.3 19.8 1.0
O A:HOH1025 4.3 20.7 1.0
O A:HOH1159 4.4 17.9 1.0
O A:HOH1082 4.4 22.8 1.0
O5' A:ADP901 4.5 16.4 1.0
O A:HOH1015 4.5 21.0 1.0
CG2 A:THR327 4.5 19.5 1.0
O2B A:ADP901 4.6 21.2 1.0
C5' A:ADP901 4.6 17.0 1.0
OG1 A:THR327 4.7 21.9 1.0
C1 A:SIN902 4.7 29.5 1.0
O1 A:SIN902 4.7 25.9 1.0
O A:HOH1075 4.7 22.6 1.0
C2 A:SIN902 4.8 21.5 1.0
CG A:ASP177 5.0 24.7 1.0
O2 A:SIN902 5.0 22.4 1.0

Manganese binding site 2 out of 15 in 8f6m

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Manganese binding site 2 out of 15 in the Complex of Rabbit Muscle Pyruvate Kinase with Adp and the Phosphonate Analogue of Pep Mimicking the Michaelis Complex.


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Complex of Rabbit Muscle Pyruvate Kinase with Adp and the Phosphonate Analogue of Pep Mimicking the Michaelis Complex. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn904

b:21.2
occ:1.00
 OE1 A:GLU271 2.1 18.7 1.0
O A:HOH1075 2.1 22.6 1.0
OD2 A:ASP295 2.2 19.5 1.0
O A:HOH1046 2.2 19.5 1.0
O2 A:SIN902 2.2 22.4 1.0
O1 A:SIN902 2.5 25.9 1.0
C1 A:SIN902 2.7 29.5 1.0
CD A:GLU271 3.1 19.1 1.0
CG A:ASP295 3.2 22.8 1.0
OE2 A:GLU271 3.4 19.2 1.0
CB A:ASP295 3.6 20.8 1.0
O A:HOH1015 4.0 21.0 1.0
O A:HOH1082 4.1 22.8 1.0
NZ A:LYS269 4.1 17.6 1.0
CZ A:PHE243 4.2 25.8 1.0
C2 A:SIN902 4.2 21.5 1.0
CE2 A:PHE243 4.2 26.4 1.0
OD1 A:ASP295 4.3 26.1 1.0
N A:ASP295 4.3 19.1 1.0
O A:HOH1308 4.5 34.3 1.0
CG A:GLU271 4.5 17.8 1.0
O A:HOH1060 4.5 21.5 1.0
O A:HOH1031 4.6 16.0 1.0
CA A:ASP295 4.6 17.3 1.0
CE A:LYS269 4.6 15.2 1.0
CB A:GLU271 4.7 19.2 1.0
CB A:ALA292 4.7 15.4 1.0
O4 A:SIN902 4.7 26.4 1.0
C3 A:SIN902 4.8 18.6 1.0
CE1 A:PHE243 4.9 24.4 1.0

Manganese binding site 3 out of 15 in 8f6m

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Manganese binding site 3 out of 15 in the Complex of Rabbit Muscle Pyruvate Kinase with Adp and the Phosphonate Analogue of Pep Mimicking the Michaelis Complex.


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Complex of Rabbit Muscle Pyruvate Kinase with Adp and the Phosphonate Analogue of Pep Mimicking the Michaelis Complex. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn1003

b:21.5
occ:1.00
 OD2 B:ASP295 2.2 20.8 1.0
O B:HOH1281 2.2 24.4 1.0
O2 B:SIN1002 2.2 19.3 1.0
OE1 B:GLU271 2.3 22.1 1.0
O B:HOH1133 2.3 18.7 1.0
O1 B:SIN1002 2.4 19.9 1.0
C1 B:SIN1002 2.6 25.8 1.0
CG B:ASP295 3.2 20.7 1.0
CD B:GLU271 3.3 21.4 1.0
OE2 B:GLU271 3.6 19.2 1.0
CB B:ASP295 3.7 19.2 1.0
O B:HOH1195 3.9 19.3 1.0
NZ B:LYS269 4.1 17.9 1.0
C2 B:SIN1002 4.1 22.9 1.0
O B:HOH1206 4.2 19.1 1.0
CZ B:PHE243 4.2 21.1 1.0
O B:HOH1331 4.3 37.5 1.0
OD1 B:ASP295 4.3 26.3 1.0
N B:ASP295 4.3 18.6 1.0
CE2 B:PHE243 4.4 21.5 1.0
O B:HOH1114 4.4 17.1 1.0
CE B:LYS269 4.5 15.9 1.0
O B:HOH1188 4.5 16.3 1.0
CG B:GLU271 4.6 16.0 1.0
CA B:ASP295 4.6 18.6 1.0
O4 B:SIN1002 4.6 23.4 1.0
CB B:ALA292 4.7 15.6 1.0
CB B:GLU271 4.8 22.2 1.0
C3 B:SIN1002 4.8 18.9 1.0
CE1 B:PHE243 4.9 22.9 1.0
C4 B:SIN1002 5.0 25.9 1.0

Manganese binding site 4 out of 15 in 8f6m

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Manganese binding site 4 out of 15 in the Complex of Rabbit Muscle Pyruvate Kinase with Adp and the Phosphonate Analogue of Pep Mimicking the Michaelis Complex.


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Complex of Rabbit Muscle Pyruvate Kinase with Adp and the Phosphonate Analogue of Pep Mimicking the Michaelis Complex. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn1005

b:20.1
occ:1.00
 O1A B:ADP1001 2.0 15.9 1.0
O1B B:ADP1001 2.1 18.7 1.0
O B:HOH1370 2.3 23.4 1.0
O B:HOH1114 2.3 17.1 1.0
O4 B:SIN1002 2.3 23.4 1.0
O3 B:SIN1002 2.4 20.4 1.0
C4 B:SIN1002 2.7 25.9 1.0
PB B:ADP1001 3.2 17.7 1.0
PA B:ADP1001 3.3 17.2 1.0
O3A B:ADP1001 3.6 20.7 1.0
O2B B:ADP1001 3.7 20.8 1.0
OD2 B:ASP177 4.0 21.6 1.0
O B:HOH1146 4.2 22.0 1.0
C3 B:SIN1002 4.2 18.9 1.0
CB B:SER361 4.2 16.7 1.0
O B:HOH1206 4.2 19.1 1.0
O2A B:ADP1001 4.2 18.8 1.0
OG B:SER361 4.3 19.0 1.0
O B:HOH1216 4.3 17.1 1.0
O5' B:ADP1001 4.4 18.6 1.0
O B:HOH1110 4.5 22.8 1.0
O B:HOH1195 4.5 19.3 1.0
O B:HOH1281 4.5 24.4 1.0
C1 B:SIN1002 4.5 25.8 1.0
CG2 B:THR327 4.5 16.5 1.0
C5' B:ADP1001 4.6 17.1 1.0
O3B B:ADP1001 4.6 19.6 1.0
O1 B:SIN1002 4.6 19.9 1.0
C2 B:SIN1002 4.6 22.9 1.0
OG1 B:THR327 4.8 22.9 1.0
O2 B:SIN1002 4.9 19.3 1.0

Manganese binding site 5 out of 15 in 8f6m

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Manganese binding site 5 out of 15 in the Complex of Rabbit Muscle Pyruvate Kinase with Adp and the Phosphonate Analogue of Pep Mimicking the Michaelis Complex.


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Complex of Rabbit Muscle Pyruvate Kinase with Adp and the Phosphonate Analogue of Pep Mimicking the Michaelis Complex. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn1003

b:33.4
occ:1.00
 O2A C:ADP1001 2.2 27.1 1.0
O C:HOH1291 2.2 28.8 1.0
O4 C:SIN1002 2.2 35.0 1.0
O1B C:ADP1001 2.3 33.5 1.0
O3 C:SIN1002 2.3 30.5 1.0
O C:HOH1102 2.4 35.0 1.0
C4 C:SIN1002 2.6 44.5 1.0
PB C:ADP1001 3.3 36.3 1.0
PA C:ADP1001 3.4 28.9 1.0
O3A C:ADP1001 3.6 35.4 1.0
O2B C:ADP1001 3.8 35.7 1.0
OD2 C:ASP177 3.9 35.7 1.0
O C:HOH1131 4.1 37.9 1.0
C3 C:SIN1002 4.1 29.4 1.0
O C:HOH1228 4.1 36.6 1.0
OG C:SER361 4.3 26.7 1.0
O C:HOH1112 4.3 30.0 1.0
O C:HOH1121 4.3 26.2 1.0
CB C:SER361 4.3 24.4 1.0
O1A C:ADP1001 4.4 32.4 1.0
C1 C:SIN1002 4.4 39.2 1.0
O5' C:ADP1001 4.5 26.7 1.0
O C:HOH1229 4.5 31.9 1.0
O C:HOH1299 4.5 27.7 1.0
O1 C:SIN1002 4.5 34.9 1.0
C5' C:ADP1001 4.5 27.1 1.0
OG1 C:THR327 4.5 28.1 1.0
C2 C:SIN1002 4.6 32.4 1.0
O3B C:ADP1001 4.6 45.3 1.0
CG2 C:THR327 4.6 20.7 1.0
O2 C:SIN1002 4.7 40.0 1.0
CG C:ASP177 4.9 39.1 1.0

Manganese binding site 6 out of 15 in 8f6m

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Manganese binding site 6 out of 15 in the Complex of Rabbit Muscle Pyruvate Kinase with Adp and the Phosphonate Analogue of Pep Mimicking the Michaelis Complex.


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Complex of Rabbit Muscle Pyruvate Kinase with Adp and the Phosphonate Analogue of Pep Mimicking the Michaelis Complex. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn1004

b:30.1
occ:1.00
 O2 C:SIN1002 2.0 40.0 1.0
OE1 C:GLU271 2.1 27.8 1.0
OD2 C:ASP295 2.1 31.1 1.0
O C:HOH1229 2.1 31.9 1.0
O C:HOH1174 2.3 23.4 1.0
O1 C:SIN1002 2.7 34.9 1.0
C1 C:SIN1002 2.7 39.2 1.0
CD C:GLU271 3.2 29.9 1.0
CG C:ASP295 3.2 33.7 1.0
OE2 C:GLU271 3.6 27.7 1.0
CB C:ASP295 3.6 26.5 1.0
O C:HOH1121 3.9 26.2 1.0
NZ C:LYS269 4.0 25.8 1.0
O C:HOH1131 4.1 37.9 1.0
C2 C:SIN1002 4.2 32.4 1.0
CZ C:PHE243 4.2 31.9 1.0
OD1 C:ASP295 4.3 35.4 1.0
CE2 C:PHE243 4.4 29.5 1.0
N C:ASP295 4.4 24.3 1.0
O C:HOH1145 4.4 27.7 1.0
O C:HOH1102 4.4 35.0 1.0
O4 C:SIN1002 4.5 35.0 1.0
CG C:GLU271 4.5 23.4 1.0
CE C:LYS269 4.6 23.3 1.0
CA C:ASP295 4.6 26.8 1.0
CB C:GLU271 4.7 33.4 1.0
CB C:ALA292 4.8 19.4 1.0
C3 C:SIN1002 4.8 29.4 1.0
C4 C:SIN1002 5.0 44.5 1.0
CE1 C:PHE243 5.0 30.6 1.0

Manganese binding site 7 out of 15 in 8f6m

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Manganese binding site 7 out of 15 in the Complex of Rabbit Muscle Pyruvate Kinase with Adp and the Phosphonate Analogue of Pep Mimicking the Michaelis Complex.


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Complex of Rabbit Muscle Pyruvate Kinase with Adp and the Phosphonate Analogue of Pep Mimicking the Michaelis Complex. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn1003

b:27.1
occ:1.00
 O1A D:ADP1001 2.1 26.8 1.0
O2B D:ADP1001 2.1 28.1 1.0
O3 D:SIN1002 2.1 29.2 1.0
O D:HOH1115 2.2 25.5 1.0
O D:HOH1321 2.2 28.1 1.0
O4 D:SIN1002 2.4 23.0 1.0
C4 D:SIN1002 2.6 31.9 1.0
PB D:ADP1001 3.3 25.6 1.0
PA D:ADP1001 3.4 23.5 1.0
O3A D:ADP1001 3.7 27.2 1.0
O1B D:ADP1001 3.9 25.0 1.0
OD2 D:ASP177 3.9 24.3 1.0
O D:HOH1172 4.0 32.7 1.0
O D:HOH1258 4.0 28.4 1.0
O D:HOH1101 4.0 28.0 1.0
C3 D:SIN1002 4.1 25.0 1.0
OG D:SER361 4.2 21.5 1.0
O D:HOH1237 4.2 25.3 1.0
O2A D:ADP1001 4.3 23.4 1.0
CB D:SER361 4.3 19.8 1.0
CG2 D:THR327 4.4 19.9 1.0
O D:HOH1120 4.4 27.8 1.0
O5' D:ADP1001 4.5 25.6 1.0
C2 D:SIN1002 4.5 25.6 1.0
C1 D:SIN1002 4.6 31.7 1.0
O3B D:ADP1001 4.6 25.0 1.0
C5' D:ADP1001 4.6 24.4 1.0
OG1 D:THR327 4.6 25.0 1.0
O1 D:SIN1002 4.8 30.7 1.0
O D:HOH1139 4.9 27.4 1.0
O2 D:SIN1002 4.9 28.7 1.0
CG D:ASP177 5.0 26.6 1.0

Manganese binding site 8 out of 15 in 8f6m

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Manganese binding site 8 out of 15 in the Complex of Rabbit Muscle Pyruvate Kinase with Adp and the Phosphonate Analogue of Pep Mimicking the Michaelis Complex.


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Complex of Rabbit Muscle Pyruvate Kinase with Adp and the Phosphonate Analogue of Pep Mimicking the Michaelis Complex. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn1004

b:22.7
occ:1.00
 O D:HOH1139 2.0 27.4 1.0
OD2 D:ASP295 2.0 25.6 1.0
OE1 D:GLU271 2.1 22.0 1.0
O D:HOH1117 2.3 21.5 1.0
O2 D:SIN1002 2.3 28.7 1.0
O1 D:SIN1002 2.4 30.7 1.0
C1 D:SIN1002 2.7 31.7 1.0
CG D:ASP295 3.1 28.3 1.0
CD D:GLU271 3.1 20.5 1.0
OE2 D:GLU271 3.4 22.2 1.0
CB D:ASP295 3.6 20.7 1.0
O D:HOH1120 4.1 27.8 1.0
NZ D:LYS269 4.1 19.6 1.0
C2 D:SIN1002 4.2 25.6 1.0
OD1 D:ASP295 4.2 26.3 1.0
CZ D:PHE243 4.2 21.5 1.0
O D:HOH1258 4.2 28.4 1.0
CE2 D:PHE243 4.3 29.0 1.0
N D:ASP295 4.3 19.6 1.0
CE D:LYS269 4.5 20.6 1.0
CG D:GLU271 4.5 21.0 1.0
O D:HOH1115 4.5 25.5 1.0
O D:HOH1218 4.5 21.6 1.0
CA D:ASP295 4.6 20.6 1.0
CB D:ALA292 4.7 20.7 1.0
CB D:GLU271 4.7 20.9 1.0
O D:HOH1326 4.7 45.6 1.0
O3 D:SIN1002 4.8 29.2 1.0
C3 D:SIN1002 4.9 25.0 1.0
CE1 D:PHE243 4.9 24.9 1.0

Manganese binding site 9 out of 15 in 8f6m

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Manganese binding site 9 out of 15 in the Complex of Rabbit Muscle Pyruvate Kinase with Adp and the Phosphonate Analogue of Pep Mimicking the Michaelis Complex.


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 9 of Complex of Rabbit Muscle Pyruvate Kinase with Adp and the Phosphonate Analogue of Pep Mimicking the Michaelis Complex. within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mn602

b:25.2
occ:1.00
 OD2 E:ASP295 1.9 27.9 1.0
OAC E:GZ3601 2.2 36.6 1.0
OE1 E:GLU271 2.2 20.1 1.0
O E:HOH783 2.3 28.9 1.0
O E:HOH983 2.3 26.9 1.0
O E:HOH968 2.4 25.2 1.0
CG E:ASP295 3.1 26.5 1.0
CD E:GLU271 3.2 19.6 1.0
OE2 E:GLU271 3.5 18.0 1.0
PAJ E:GZ3601 3.5 33.8 1.0
O E:HOH776 3.7 17.1 1.0
CB E:ASP295 3.8 23.7 1.0
CAG E:GZ3601 3.9 22.9 1.0
O E:HOH1008 4.0 34.5 1.0
OD1 E:ASP295 4.1 27.8 1.0
OAE E:GZ3601 4.2 34.4 1.0
O E:HOH772 4.2 20.6 1.0
O E:HOH974 4.3 18.8 1.0
CG E:GLU271 4.6 17.5 1.0
O E:HOH798 4.6 25.0 1.0
O E:HOH736 4.7 29.9 1.0
OAF E:GZ3601 4.7 28.7 1.0
CB E:GLU271 4.7 14.3 1.0
O E:HOH919 4.8 31.6 1.0
O1 E:GOL609 4.9 31.6 1.0

Manganese binding site 10 out of 15 in 8f6m

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Manganese binding site 10 out of 15 in the Complex of Rabbit Muscle Pyruvate Kinase with Adp and the Phosphonate Analogue of Pep Mimicking the Michaelis Complex.


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 10 of Complex of Rabbit Muscle Pyruvate Kinase with Adp and the Phosphonate Analogue of Pep Mimicking the Michaelis Complex. within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mn603

b:47.5
occ:1.00
 OAE E:GZ3601 2.3 34.4 1.0
O E:HOH1046 2.5 34.1 1.0
OAB E:GZ3601 2.5 24.1 1.0
OD1 E:ASP295 2.6 27.8 1.0
O E:HOH1043 2.7 41.0 1.0
CAI E:GZ3601 3.4 16.6 1.0
CG E:ASP295 3.4 26.5 1.0
O E:HOH776 3.5 17.1 1.0
PAJ E:GZ3601 3.6 33.8 1.0
N E:ASP295 3.7 17.6 1.0
OD2 E:ASP295 3.9 27.9 1.0
CAG E:GZ3601 3.9 22.9 1.0
CAH E:GZ3601 3.9 27.1 1.0
CA E:GLY294 4.2 18.2 1.0
C E:GLY294 4.2 25.6 1.0
OAD E:GZ3601 4.3 25.3 1.0
O E:HOH837 4.4 40.2 1.0
OAC E:GZ3601 4.4 36.6 1.0
CB E:ASP295 4.4 23.7 1.0
O E:HOH964 4.5 28.1 1.0
O E:HOH1090 4.5 38.0 1.0
CA E:ASP295 4.5 21.1 1.0
OAF E:GZ3601 4.7 28.7 1.0
CAA E:GZ3601 4.9 21.5 1.0
CG2 E:THR327 5.0 16.1 1.0
O E:HOH777 5.0 20.0 1.0
N E:GLY294 5.0 15.8 1.0

Reference:

L.Swint-Kruse, L.L.Dougherty, B.Page, T.Wu, P.T.O'neil, C.B.Prasannan, C.Timmons, Q.Tang, D.J.Parente, S.Sreenivasan, T.Holyoak, A.W.Fenton. Pyk-Substitutionome: An Integrated Database Containing Allosteric Coupling, Ligand Affinity and Mutational, Structural, Pathological, Bioinformatic and Computational Information About Pyruvate Kinase Isozymes. Database (Oxford) V.2023 2023.
ISSN: ISSN 1758-0463
PubMed: 37171062
DOI: 10.1093/DATABASE/BAAD030
Page generated: Sun Oct 6 12:06:36 2024

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