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Manganese in PDB 8odo: Structure of Human Guanylylated Rtcb in Complex with Archease

Enzymatic activity of Structure of Human Guanylylated Rtcb in Complex with Archease

All present enzymatic activity of Structure of Human Guanylylated Rtcb in Complex with Archease:
6.5.1.8;

Protein crystallography data

The structure of Structure of Human Guanylylated Rtcb in Complex with Archease, PDB code: 8odo was solved by J.Kopp, J.L.Gerber, J.Peschek, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 75.23 / 2.20
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 99.09, 125.547, 125.733, 90, 108.51, 90
R / Rfree (%) 19.3 / 21.8

Manganese Binding Sites:

The binding sites of Manganese atom in the Structure of Human Guanylylated Rtcb in Complex with Archease (pdb code 8odo). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 8 binding sites of Manganese where determined in the Structure of Human Guanylylated Rtcb in Complex with Archease, PDB code: 8odo:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 8odo

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Manganese binding site 1 out of 8 in the Structure of Human Guanylylated Rtcb in Complex with Archease


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Structure of Human Guanylylated Rtcb in Complex with Archease within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn602

b:67.2
occ:1.00
 O1P A:5GP601 2.2 44.9 1.0
O A:HOH731 2.2 56.3 1.0
NE2 A:HIS259 2.2 49.7 1.0
NE2 A:HIS353 2.2 49.4 1.0
SG A:CYS122 2.5 45.0 1.0
CE1 A:HIS259 2.9 47.7 1.0
CE1 A:HIS353 3.1 46.2 1.0
CD2 A:HIS353 3.3 46.5 1.0
CD2 A:HIS259 3.4 49.8 1.0
CB A:CYS122 3.5 47.4 1.0
P A:5GP601 3.5 47.3 1.0
ND1 A:HIS259 4.1 49.9 1.0
ND1 A:HIS353 4.3 48.5 1.0
CD2 A:HIS428 4.3 42.7 1.0
NE2 A:HIS227 4.3 43.6 1.0
NE2 A:HIS428 4.3 50.0 1.0
CG A:HIS353 4.4 47.6 1.0
CG A:HIS259 4.4 45.0 1.0
CD2 A:HIS227 4.4 51.4 1.0
C5' A:5GP601 4.6 48.0 1.0
O5' A:5GP601 4.6 49.0 1.0
O3P A:5GP601 4.6 44.7 1.0
O2 A:PO4603 4.6 52.3 1.0
OD2 A:ASP119 4.7 48.8 1.0
CA A:CYS122 4.7 46.2 1.0
C A:CYS122 4.7 49.4 1.0
ND2 A:ASN354 4.9 46.8 1.0
N A:GLY123 5.0 46.7 1.0
O A:CYS122 5.0 44.8 1.0

Manganese binding site 2 out of 8 in 8odo

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Manganese binding site 2 out of 8 in the Structure of Human Guanylylated Rtcb in Complex with Archease


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Structure of Human Guanylylated Rtcb in Complex with Archease within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn201

b:44.6
occ:1.00
 O B:HOH326 2.1 53.9 1.0
O B:ILE179 2.1 56.8 1.0
OD1 B:ASP178 2.2 43.0 1.0
O B:HOH335 2.2 43.6 1.0
O1 A:PO4603 2.2 56.8 1.0
OD1 B:ASP51 2.2 52.9 1.0
CG B:ASP51 3.2 51.6 1.0
C B:ILE179 3.3 52.7 1.0
P A:PO4603 3.3 47.4 1.0
CG B:ASP178 3.4 45.8 1.0
O4 A:PO4603 3.4 44.6 1.0
N B:ILE179 3.5 44.4 1.0
OD2 B:ASP51 3.6 45.4 1.0
O3 A:PO4603 4.0 43.5 1.0
CA B:ILE179 4.0 45.5 1.0
OD2 B:ASP178 4.1 45.8 1.0
O A:HOH837 4.1 46.1 1.0
NZ B:LYS156 4.1 43.5 1.0
C B:ASP178 4.2 41.9 1.0
OXT B:ILE179 4.2 48.5 1.0
CA B:ASP178 4.3 43.1 1.0
O B:ALA50 4.4 46.7 1.0
CD B:LYS156 4.4 45.2 1.0
CB B:ASP178 4.4 41.5 1.0
O2 A:PO4603 4.6 52.3 1.0
CB B:ASP51 4.6 43.3 1.0
CE2 A:TYR92 4.6 47.1 1.0
CE B:LYS156 4.6 47.9 1.0
CG1 B:ILE179 4.8 48.6 1.0

Manganese binding site 3 out of 8 in 8odo

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Manganese binding site 3 out of 8 in the Structure of Human Guanylylated Rtcb in Complex with Archease


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Structure of Human Guanylylated Rtcb in Complex with Archease within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn602

b:51.6
occ:1.00
 O3P C:5GP601 2.2 49.7 1.0
NE2 C:HIS259 2.3 48.9 1.0
O C:HOH710 2.3 55.3 1.0
NE2 C:HIS353 2.3 51.6 1.0
SG C:CYS122 2.5 48.6 1.0
CE1 C:HIS353 3.1 47.3 1.0
CE1 C:HIS259 3.1 48.4 1.0
CD2 C:HIS259 3.4 45.4 1.0
CD2 C:HIS353 3.4 49.4 1.0
P C:5GP601 3.6 49.0 1.0
CB C:CYS122 3.6 46.0 1.0
CD2 C:HIS428 4.3 49.6 1.0
ND1 C:HIS353 4.3 49.3 1.0
NE2 C:HIS428 4.3 50.4 1.0
ND1 C:HIS259 4.3 50.0 1.0
OD1 C:ASN226 4.4 48.2 1.0
CG C:HIS259 4.4 47.4 1.0
CG C:HIS353 4.5 46.8 1.0
O2 C:PO4603 4.5 42.0 1.0
OD2 C:ASP119 4.5 52.6 1.0
NE2 C:HIS227 4.5 45.2 1.0
CD2 C:HIS227 4.6 52.2 1.0
C5' C:5GP601 4.6 49.8 1.0
O1P C:5GP601 4.6 46.3 1.0
O5' C:5GP601 4.6 50.1 1.0
C C:CYS122 4.7 49.7 1.0
CA C:CYS122 4.8 46.9 1.0
O C:HOH794 4.9 49.4 1.0
O C:CYS122 5.0 48.6 1.0

Manganese binding site 4 out of 8 in 8odo

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Manganese binding site 4 out of 8 in the Structure of Human Guanylylated Rtcb in Complex with Archease


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Structure of Human Guanylylated Rtcb in Complex with Archease within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn201

b:48.5
occ:1.00
 OD1 D:ASP178 2.1 55.9 1.0
O1 C:PO4603 2.2 52.2 1.0
OD1 D:ASP51 2.2 44.9 1.0
O C:HOH704 2.2 54.0 1.0
O D:ILE179 2.2 46.6 1.0
O D:HOH346 2.2 53.1 1.0
CG D:ASP51 3.1 45.4 1.0
OD2 D:ASP51 3.3 51.0 1.0
P C:PO4603 3.3 52.7 1.0
CG D:ASP178 3.3 47.1 1.0
C D:ILE179 3.4 53.5 1.0
O4 C:PO4603 3.4 45.9 1.0
N D:ILE179 3.5 47.7 1.0
OD2 D:ASP178 4.0 42.7 1.0
NZ D:LYS156 4.0 54.6 1.0
O C:HOH858 4.1 50.1 1.0
CA D:ILE179 4.1 47.6 1.0
O3 C:PO4603 4.2 45.5 1.0
C D:ASP178 4.3 47.9 1.0
OXT D:ILE179 4.3 52.3 1.0
CA D:ASP178 4.4 46.2 1.0
CB D:ASP178 4.4 45.1 1.0
O2 C:PO4603 4.4 42.0 1.0
CD D:LYS156 4.5 45.8 1.0
O D:ALA50 4.5 40.2 1.0
CB D:ASP51 4.5 39.9 1.0
CE2 C:TYR92 4.6 39.8 1.0
CE D:LYS156 4.7 47.5 1.0
CG1 D:ILE179 4.8 48.3 1.0

Manganese binding site 5 out of 8 in 8odo

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Manganese binding site 5 out of 8 in the Structure of Human Guanylylated Rtcb in Complex with Archease


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Structure of Human Guanylylated Rtcb in Complex with Archease within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mn602

b:79.9
occ:1.00
 O3P E:5GP601 2.2 74.1 1.0
NE2 E:HIS259 2.2 66.5 1.0
O E:HOH712 2.2 73.0 1.0
NE2 E:HIS353 2.2 80.0 1.0
SG E:CYS122 2.5 73.5 1.0
CE1 E:HIS259 2.8 66.7 1.0
CE1 E:HIS353 2.9 78.3 1.0
CD2 E:HIS353 3.4 77.9 1.0
CD2 E:HIS259 3.4 74.5 1.0
CB E:CYS122 3.6 71.5 1.0
P E:5GP601 3.6 71.2 1.0
ND1 E:HIS259 4.0 71.0 1.0
O4 E:PO4603 4.1 67.3 1.0
ND1 E:HIS353 4.1 77.7 1.0
NE2 E:HIS428 4.3 78.4 1.0
CG E:HIS259 4.4 72.3 1.0
O E:HOH705 4.4 66.6 1.0
CG E:HIS353 4.4 79.4 1.0
NE2 E:HIS227 4.4 74.8 1.0
CD2 E:HIS428 4.5 78.3 1.0
CD2 E:HIS227 4.5 74.1 1.0
OD2 E:ASP119 4.5 69.1 1.0
O1P E:5GP601 4.5 70.4 1.0
O5' E:5GP601 4.6 65.4 1.0
C5' E:5GP601 4.6 67.8 1.0
C E:CYS122 4.8 78.0 1.0
CA E:CYS122 4.8 73.6 1.0
ND2 E:ASN354 4.8 78.4 1.0
O E:CYS122 5.0 80.5 1.0

Manganese binding site 6 out of 8 in 8odo

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Manganese binding site 6 out of 8 in the Structure of Human Guanylylated Rtcb in Complex with Archease


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Structure of Human Guanylylated Rtcb in Complex with Archease within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mn201

b:55.9
occ:1.00
 O2 E:PO4603 2.1 65.2 1.0
OD1 F:ASP178 2.2 58.1 1.0
O F:HOH304 2.2 59.9 1.0
OD1 F:ASP51 2.2 57.1 1.0
O F:ILE179 2.2 64.7 1.0
O F:HOH311 2.2 54.7 1.0
CG F:ASP51 3.1 55.4 1.0
P E:PO4603 3.3 62.6 1.0
OD2 F:ASP51 3.3 59.3 1.0
C F:ILE179 3.4 62.2 1.0
O1 E:PO4603 3.4 65.3 1.0
CG F:ASP178 3.4 57.9 1.0
N F:ILE179 3.4 57.9 1.0
CA F:ILE179 4.0 58.5 1.0
OD2 F:ASP178 4.1 59.3 1.0
C F:ASP178 4.2 56.2 1.0
O3 E:PO4603 4.2 66.7 1.0
O4 E:PO4603 4.3 67.3 1.0
OXT F:ILE179 4.3 64.5 1.0
CA F:ASP178 4.3 57.7 1.0
O F:ALA50 4.3 55.0 1.0
NZ F:LYS156 4.4 69.0 1.0
CB F:ASP178 4.4 57.0 1.0
CE2 E:TYR92 4.5 58.4 1.0
CB F:ASP51 4.5 47.3 1.0
CG1 F:ILE179 4.7 54.1 1.0
CD F:LYS156 4.7 63.5 1.0
CE F:LYS156 5.0 63.4 1.0
C F:ALA50 5.0 55.0 1.0

Manganese binding site 7 out of 8 in 8odo

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Manganese binding site 7 out of 8 in the Structure of Human Guanylylated Rtcb in Complex with Archease


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Structure of Human Guanylylated Rtcb in Complex with Archease within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mn602

b:52.9
occ:1.00
 O3P G:5GP601 2.2 41.2 1.0
NE2 G:HIS259 2.2 58.7 1.0
O G:HOH744 2.2 60.6 1.0
NE2 G:HIS353 2.3 55.6 1.0
SG G:CYS122 2.5 55.1 1.0
CE1 G:HIS259 3.0 60.8 1.0
CD2 G:HIS353 3.2 58.6 1.0
CD2 G:HIS259 3.3 57.5 1.0
CE1 G:HIS353 3.4 59.8 1.0
CB G:CYS122 3.5 56.9 1.0
P G:5GP601 3.5 56.0 1.0
ND1 G:HIS259 4.2 64.0 1.0
NE2 G:HIS428 4.3 57.6 1.0
OD1 G:ASN226 4.3 63.3 1.0
CD2 G:HIS428 4.3 52.3 1.0
CG G:HIS353 4.4 59.5 1.0
CG G:HIS259 4.4 61.1 1.0
O1 G:PO4603 4.4 60.7 1.0
O1P G:5GP601 4.4 53.6 1.0
NE2 G:HIS227 4.4 63.1 1.0
ND1 G:HIS353 4.5 62.9 1.0
ND2 G:ASN354 4.5 56.6 1.0
OD2 G:ASP119 4.6 56.7 1.0
CD2 G:HIS227 4.6 60.6 1.0
C5' G:5GP601 4.6 57.8 1.0
O5' G:5GP601 4.6 53.6 1.0
CA G:CYS122 4.7 54.8 1.0
C G:CYS122 4.7 58.4 1.0
O G:CYS122 4.9 57.4 1.0
CG G:ASN226 5.0 61.0 1.0
O G:HOH704 5.0 54.1 1.0

Manganese binding site 8 out of 8 in 8odo

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Manganese binding site 8 out of 8 in the Structure of Human Guanylylated Rtcb in Complex with Archease


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Structure of Human Guanylylated Rtcb in Complex with Archease within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mn201

b:101.0
occ:1.00
 O H:HOH308 2.1 55.7 1.0
OD1 H:ASP178 2.1 52.0 1.0
O2 G:PO4603 2.2 63.9 1.0
O H:ILE179 2.2 62.1 1.0
OD1 H:ASP51 2.2 62.2 1.0
O H:HOH303 2.2 61.7 1.0
CG H:ASP51 3.1 54.7 1.0
O3 G:PO4603 3.3 49.4 1.0
P G:PO4603 3.3 52.0 1.0
C H:ILE179 3.3 57.0 1.0
OD2 H:ASP51 3.4 50.8 1.0
CG H:ASP178 3.4 52.0 1.0
N H:ILE179 3.5 43.4 1.0
CA H:ILE179 4.0 51.8 1.0
O4 G:PO4603 4.1 48.3 1.0
OD2 H:ASP178 4.1 49.8 1.0
C H:ASP178 4.2 49.0 1.0
OXT H:ILE179 4.3 59.6 1.0
NZ H:LYS156 4.3 60.5 1.0
CA H:ASP178 4.3 51.6 1.0
O H:ALA50 4.4 57.2 1.0
CB H:ASP178 4.4 50.7 1.0
O1 G:PO4603 4.4 60.7 1.0
CE2 G:TYR92 4.5 51.3 1.0
CB H:ASP51 4.5 56.1 1.0
CD H:LYS156 4.6 53.8 1.0
CG1 H:ILE179 4.7 57.8 1.0
CE H:LYS156 4.9 57.5 1.0

Reference:

J.L.Gerber, J.Kopp, J.Peschek. Structure of Human Rtcb in Complex with Archease To Be Published.
Page generated: Sun Oct 6 13:28:51 2024

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