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Manganese in PDB 1kgp: R2F From Corynebacterium Ammoniagenes in Its Mn Substituted Form

Protein crystallography data

The structure of R2F From Corynebacterium Ammoniagenes in Its Mn Substituted Form, PDB code: 1kgp was solved by M.Hogbom, Y.Huque, B.M.Sjoberg, P.Nordlund, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.00 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.670, 91.196, 137.270, 90.00, 91.45, 90.00
R / Rfree (%) 17.7 / 23.6

Manganese Binding Sites:

The binding sites of Manganese atom in the R2F From Corynebacterium Ammoniagenes in Its Mn Substituted Form (pdb code 1kgp). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 10 binding sites of Manganese where determined in the R2F From Corynebacterium Ammoniagenes in Its Mn Substituted Form, PDB code: 1kgp:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Manganese binding site 1 out of 10 in 1kgp

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Manganese binding site 1 out of 10 in the R2F From Corynebacterium Ammoniagenes in Its Mn Substituted Form


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Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of R2F From Corynebacterium Ammoniagenes in Its Mn Substituted Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn1001

b:15.1
occ:0.30
 OD1 A:ASP77 1.9 33.2 1.0
OE1 A:GLU202 2.0 37.1 1.0
ND1 A:HIS111 2.1 16.8 1.0
OE1 A:GLU108 2.4 32.2 1.0
CD A:GLU202 2.8 36.2 1.0
OE2 A:GLU108 2.8 31.1 1.0
CD A:GLU108 2.9 29.6 1.0
OE2 A:GLU202 3.0 38.4 1.0
CG A:ASP77 3.0 33.4 1.0
CE1 A:HIS111 3.1 16.6 1.0
CG A:HIS111 3.2 15.3 1.0
CB A:HIS111 3.5 16.4 1.0
CZ A:PHE172 3.6 20.6 1.0
OD2 A:ASP77 3.7 33.7 1.0
MN A:MN1002 3.9 19.0 0.4
O A:HOH1163 4.0 35.1 1.0
CE2 A:PHE172 4.0 20.1 1.0
CG A:GLU202 4.1 31.9 1.0
CB A:ASP77 4.2 23.7 1.0
NE2 A:HIS111 4.2 14.9 1.0
CD2 A:HIS111 4.3 17.2 1.0
CG A:GLU108 4.3 21.0 1.0
CG2 A:ILE198 4.3 14.8 1.0
CA A:GLU108 4.4 17.1 1.0
CE1 A:PHE172 4.4 21.3 1.0
CA A:ASP77 4.7 19.4 1.0
CB A:GLU108 4.7 17.9 1.0
OE1 A:GLU168 4.8 38.6 1.0
O A:GLU108 4.9 18.6 1.0

Manganese binding site 2 out of 10 in 1kgp

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Manganese binding site 2 out of 10 in the R2F From Corynebacterium Ammoniagenes in Its Mn Substituted Form


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Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of R2F From Corynebacterium Ammoniagenes in Its Mn Substituted Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn1002

b:19.0
occ:0.40
 OE1 A:GLU168 1.9 38.6 1.0
OE2 A:GLU202 2.1 38.4 1.0
ND1 A:HIS205 2.2 18.5 1.0
OE2 A:GLU108 2.3 31.1 1.0
OE2 A:GLU168 2.3 36.3 1.0
CD A:GLU168 2.4 36.9 1.0
CE1 A:HIS205 3.1 15.0 1.0
CD A:GLU108 3.1 29.6 1.0
CG A:HIS205 3.2 16.7 1.0
CD A:GLU202 3.3 36.2 1.0
CB A:HIS205 3.6 16.4 1.0
OE1 A:GLU108 3.7 32.2 1.0
MN A:MN1001 3.9 15.1 0.3
CG A:GLU168 3.9 30.4 1.0
OE1 A:GLU202 4.0 37.1 1.0
CG A:GLU108 4.1 21.0 1.0
CA A:GLU202 4.1 20.1 1.0
NE2 A:HIS205 4.2 15.8 1.0
CD2 A:HIS205 4.3 16.4 1.0
CG A:GLU202 4.4 31.9 1.0
CB A:GLU202 4.4 20.7 1.0
CG A:GLN80 4.5 27.2 1.0
CG2 A:ILE104 4.6 13.9 1.0
CB A:GLU168 4.6 23.5 1.0
CE2 A:PHE172 4.7 20.1 1.0
N A:GLU202 4.8 15.8 1.0
CE1 A:HIS111 4.8 16.6 1.0
ND1 A:HIS111 4.9 16.8 1.0
NE2 A:GLN80 5.0 37.3 1.0

Manganese binding site 3 out of 10 in 1kgp

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Manganese binding site 3 out of 10 in the R2F From Corynebacterium Ammoniagenes in Its Mn Substituted Form


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of R2F From Corynebacterium Ammoniagenes in Its Mn Substituted Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn1003

b:16.2
occ:0.40
 OD1 B:ASP77 1.9 32.1 1.0
OE1 B:GLU202 2.0 40.3 1.0
OE1 B:GLU108 2.3 35.5 1.0
ND1 B:HIS111 2.3 17.6 1.0
CD B:GLU202 2.8 32.2 1.0
CD B:GLU108 3.0 31.4 1.0
CG B:ASP77 3.0 32.4 1.0
OE2 B:GLU202 3.1 29.7 1.0
OE2 B:GLU108 3.1 38.6 1.0
CE1 B:HIS111 3.3 16.4 1.0
CG B:HIS111 3.3 17.9 1.0
CB B:HIS111 3.6 17.9 1.0
CZ B:PHE172 3.6 25.4 1.0
OD2 B:ASP77 3.7 35.6 1.0
MN B:MN1004 3.9 18.7 0.5
CB B:ASP77 4.1 16.9 1.0
CE2 B:PHE172 4.1 19.4 1.0
O B:HOH1128 4.2 25.9 1.0
CG B:GLU202 4.2 28.1 1.0
CE1 B:PHE172 4.3 27.0 1.0
CA B:GLU108 4.3 16.7 1.0
CG B:GLU108 4.3 26.8 1.0
NE2 B:HIS111 4.4 16.4 1.0
CD2 B:HIS111 4.5 17.4 1.0
CG2 B:ILE198 4.5 15.5 1.0
CA B:ASP77 4.5 19.3 1.0
CB B:GLU108 4.6 20.3 1.0
O B:GLU108 4.9 13.8 1.0

Manganese binding site 4 out of 10 in 1kgp

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Manganese binding site 4 out of 10 in the R2F From Corynebacterium Ammoniagenes in Its Mn Substituted Form


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of R2F From Corynebacterium Ammoniagenes in Its Mn Substituted Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn1004

b:18.7
occ:0.50
 OE2 B:GLU202 1.8 29.7 1.0
OE2 B:GLU108 2.0 38.6 1.0
OE2 B:GLU168 2.3 44.3 1.0
ND1 B:HIS205 2.3 17.1 1.0
CD B:GLU202 3.1 32.2 1.0
CD B:GLU108 3.1 31.4 1.0
CE1 B:HIS205 3.1 18.3 1.0
CD B:GLU168 3.3 46.9 1.0
CG B:HIS205 3.3 19.3 1.0
OE1 B:GLU108 3.6 35.5 1.0
CB B:HIS205 3.7 17.5 1.0
OE1 B:GLU202 3.8 40.3 1.0
MN B:MN1003 3.9 16.2 0.4
CG B:GLU168 3.9 40.4 1.0
CA B:GLU202 4.0 21.7 1.0
CG B:GLU202 4.2 28.1 1.0
OE1 B:GLU168 4.2 53.9 1.0
CB B:GLU202 4.2 24.8 1.0
CG B:GLU108 4.2 26.8 1.0
NE2 B:HIS205 4.3 16.5 1.0
CD2 B:HIS205 4.4 19.4 1.0
CG B:GLN80 4.5 29.3 1.0
CE2 B:PHE172 4.5 19.4 1.0
CB B:GLU168 4.5 30.3 1.0
N B:GLU202 4.7 19.1 1.0
CE1 B:HIS111 4.7 16.4 1.0
CG2 B:ILE104 4.8 14.4 1.0
ND1 B:HIS111 4.9 17.6 1.0
NE2 B:GLN80 4.9 34.4 1.0
CZ B:PHE172 5.0 25.4 1.0

Manganese binding site 5 out of 10 in 1kgp

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Manganese binding site 5 out of 10 in the R2F From Corynebacterium Ammoniagenes in Its Mn Substituted Form


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of R2F From Corynebacterium Ammoniagenes in Its Mn Substituted Form within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn2001

b:22.0
occ:0.30
 OD1 C:ASP77 2.1 34.2 1.0
ND1 C:HIS111 2.1 16.9 1.0
OE1 C:GLU202 2.2 48.5 1.0
OE1 C:GLU108 2.6 40.6 1.0
CD C:GLU202 2.8 46.4 1.0
OE2 C:GLU202 2.8 45.3 1.0
OE2 C:GLU108 2.9 40.3 1.0
CD C:GLU108 3.0 34.0 1.0
CE1 C:HIS111 3.0 20.0 1.0
CG C:HIS111 3.1 17.1 1.0
CG C:ASP77 3.2 30.5 1.0
O C:HOH3086 3.4 49.3 1.0
CB C:HIS111 3.4 16.8 1.0
OD2 C:ASP77 3.8 37.2 1.0
MN C:MN2002 3.9 22.3 0.3
CZ C:PHE172 3.9 32.4 1.0
CE2 C:PHE172 4.0 31.5 1.0
CG C:GLU202 4.1 39.5 1.0
NE2 C:HIS111 4.2 18.6 1.0
CD2 C:HIS111 4.2 17.8 1.0
CG2 C:ILE198 4.3 18.7 1.0
CA C:GLU108 4.3 18.9 1.0
CB C:ASP77 4.4 24.8 1.0
CG C:GLU108 4.4 31.3 1.0
CE1 C:PHE172 4.5 32.8 1.0
CD2 C:PHE172 4.6 32.0 1.0
CB C:GLU108 4.7 22.2 1.0
CA C:ASP77 4.8 20.9 1.0
OE1 C:GLU168 4.9 39.0 1.0
O C:GLU108 4.9 18.0 1.0
CA C:HIS111 5.0 13.7 1.0
CD1 C:PHE172 5.0 31.8 1.0

Manganese binding site 6 out of 10 in 1kgp

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Manganese binding site 6 out of 10 in the R2F From Corynebacterium Ammoniagenes in Its Mn Substituted Form


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of R2F From Corynebacterium Ammoniagenes in Its Mn Substituted Form within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn2002

b:22.3
occ:0.30
 OE2 C:GLU202 2.0 45.3 1.0
OE2 C:GLU168 2.0 38.4 1.0
OE1 C:GLU168 2.1 39.0 1.0
ND1 C:HIS205 2.2 20.9 1.0
OE2 C:GLU108 2.2 40.3 1.0
CD C:GLU168 2.4 36.0 1.0
CD C:GLU108 3.0 34.0 1.0
CE1 C:HIS205 3.1 19.9 1.0
CD C:GLU202 3.2 46.4 1.0
CG C:HIS205 3.3 19.8 1.0
OE1 C:GLU108 3.4 40.6 1.0
CB C:HIS205 3.6 20.6 1.0
CG C:GLU168 3.9 33.2 1.0
MN C:MN2001 3.9 22.0 0.3
OE1 C:GLU202 3.9 48.5 1.0
CA C:GLU202 4.1 23.6 1.0
CG C:GLU108 4.2 31.3 1.0
NE2 C:HIS205 4.3 18.5 1.0
CG C:GLU202 4.3 39.5 1.0
CD2 C:HIS205 4.4 19.7 1.0
CB C:GLU202 4.4 27.8 1.0
CE2 C:PHE172 4.4 31.5 1.0
CE1 C:HIS111 4.6 20.0 1.0
CG2 C:ILE104 4.7 15.9 1.0
N C:GLU202 4.7 21.6 1.0
CG C:GLN80 4.7 32.7 1.0
CB C:GLU168 4.7 24.9 1.0
CD2 C:PHE172 4.8 32.0 1.0
ND1 C:HIS111 4.8 16.9 1.0
NE2 C:GLN80 5.0 39.9 1.0

Manganese binding site 7 out of 10 in 1kgp

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Manganese binding site 7 out of 10 in the R2F From Corynebacterium Ammoniagenes in Its Mn Substituted Form


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of R2F From Corynebacterium Ammoniagenes in Its Mn Substituted Form within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn3001

b:19.7
occ:0.50
 O C:HOH3073 1.9 24.0 1.0
O C:HOH3147 2.2 33.8 1.0
O D:HOH2064 2.2 31.7 1.0
O C:HOH3174 2.4 37.8 1.0
O D:HOH2037 3.0 37.3 1.0
NZ D:LYS113 4.2 21.8 1.0
OD2 C:ASP34 4.2 27.5 1.0
OE2 D:GLU44 4.3 49.0 1.0
OD1 C:ASP34 4.3 28.3 1.0
O C:HOH3148 4.5 36.6 1.0
CG C:ASP34 4.7 26.3 1.0
CG D:GLU44 4.7 41.5 1.0
CD1 C:LEU30 4.8 17.3 1.0
CD D:GLU44 4.9 46.3 1.0
CD2 C:LEU30 5.0 23.2 1.0

Manganese binding site 8 out of 10 in 1kgp

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Manganese binding site 8 out of 10 in the R2F From Corynebacterium Ammoniagenes in Its Mn Substituted Form


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of R2F From Corynebacterium Ammoniagenes in Its Mn Substituted Form within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn3002

b:24.6
occ:0.40
 OE2 C:GLU222 2.1 31.4 1.0
OE2 C:GLU226 2.3 29.4 1.0
CD C:GLU226 3.1 27.1 1.0
OE1 C:GLU226 3.2 29.3 1.0
CD C:GLU222 3.3 30.3 1.0
CG C:GLU222 3.8 23.4 1.0
O C:HOH3050 4.0 30.2 1.0
OE1 C:GLU222 4.3 31.0 1.0
CG C:GLU226 4.5 16.7 1.0

Manganese binding site 9 out of 10 in 1kgp

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Manganese binding site 9 out of 10 in the R2F From Corynebacterium Ammoniagenes in Its Mn Substituted Form


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 9 of R2F From Corynebacterium Ammoniagenes in Its Mn Substituted Form within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn2003

b:16.6
occ:0.80
 OD1 D:ASP77 1.9 24.4 1.0
OE2 D:GLU202 2.1 31.6 1.0
OE1 D:GLU108 2.1 24.7 1.0
ND1 D:HIS111 2.2 16.5 1.0
CD D:GLU202 2.8 27.0 1.0
OE1 D:GLU202 2.8 26.8 1.0
CG D:ASP77 3.0 26.2 1.0
CE1 D:HIS111 3.2 14.5 1.0
CD D:GLU108 3.2 16.2 1.0
CG D:HIS111 3.3 15.1 1.0
OE2 D:GLU108 3.6 23.0 1.0
CB D:HIS111 3.6 11.0 1.0
CZ D:PHE172 3.6 27.0 1.0
OD2 D:ASP77 3.6 27.3 1.0
MN D:MN2004 3.9 16.7 0.9
CE2 D:PHE172 4.0 30.1 1.0
CG D:GLU202 4.2 23.6 1.0
CB D:ASP77 4.2 23.7 1.0
O D:HOH2071 4.3 34.0 1.0
CG2 D:ILE198 4.3 15.9 1.0
NE2 D:HIS111 4.3 12.5 1.0
CA D:GLU108 4.3 12.7 1.0
CD2 D:HIS111 4.4 12.1 1.0
CE1 D:PHE172 4.4 28.0 1.0
CG D:GLU108 4.5 17.2 1.0
CB D:GLU108 4.6 16.3 1.0
CA D:ASP77 4.7 19.7 1.0
OE1 D:GLU168 5.0 26.8 1.0
O D:GLU108 5.0 16.7 1.0

Manganese binding site 10 out of 10 in 1kgp

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Manganese binding site 10 out of 10 in the R2F From Corynebacterium Ammoniagenes in Its Mn Substituted Form


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 10 of R2F From Corynebacterium Ammoniagenes in Its Mn Substituted Form within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn2004

b:16.7
occ:0.90
 OE1 D:GLU168 2.0 26.8 1.0
OE2 D:GLU108 2.0 23.0 1.0
OE1 D:GLU202 2.2 26.8 1.0
ND1 D:HIS205 2.2 17.3 1.0
OE2 D:GLU168 2.4 22.3 1.0
CD D:GLU168 2.5 27.2 1.0
CD D:GLU108 3.1 16.2 1.0
CE1 D:HIS205 3.1 14.9 1.0
CG D:HIS205 3.2 13.8 1.0
CD D:GLU202 3.3 27.0 1.0
OE1 D:GLU108 3.5 24.7 1.0
CB D:HIS205 3.5 16.2 1.0
MN D:MN2003 3.9 16.6 0.8
CG D:GLU168 4.0 27.5 1.0
OE2 D:GLU202 4.0 31.6 1.0
CA D:GLU202 4.1 21.9 1.0
NE2 D:HIS205 4.3 15.0 1.0
CD2 D:HIS205 4.3 13.9 1.0
CG D:GLU202 4.4 23.6 1.0
CG D:GLU108 4.4 17.2 1.0
CB D:GLU202 4.4 18.2 1.0
CG D:GLN80 4.5 32.2 1.0
CE2 D:PHE172 4.6 30.1 1.0
CG2 D:ILE104 4.6 18.3 1.0
CB D:GLU168 4.7 23.9 1.0
N D:GLU202 4.7 19.2 1.0
NE2 D:GLN80 4.7 36.4 1.0
CE1 D:HIS111 4.8 14.5 1.0
ND1 D:HIS111 4.9 16.5 1.0

Reference:

M.Hogbom, Y.Huque, B.M.Sjoberg, P.Nordlund. Crystal Structure of the Di-Iron/Radical Protein of Ribonucleotide Reductase From Corynebacterium Ammoniagenes. Biochemistry V. 41 1381 2002.
ISSN: ISSN 0006-2960
PubMed: 11802741
DOI: 10.1021/BI011429L
Page generated: Sat Oct 5 11:20:17 2024

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