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Manganese in PDB 2rcv: Crystal Structure of the Bacillus Subtilis Superoxide Dismutase

Enzymatic activity of Crystal Structure of the Bacillus Subtilis Superoxide Dismutase

All present enzymatic activity of Crystal Structure of the Bacillus Subtilis Superoxide Dismutase:
1.15.1.1;

Protein crystallography data

The structure of Crystal Structure of the Bacillus Subtilis Superoxide Dismutase, PDB code: 2rcv was solved by P.Liu, H.E.Ewis, Y.J.Huang, C.D.Lu, P.C.Tai, I.T.Weber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.90 / 1.60
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 68.369, 84.034, 91.951, 99.13, 105.98, 105.58
R / Rfree (%) 21.1 / 23

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of the Bacillus Subtilis Superoxide Dismutase (pdb code 2rcv). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 8 binding sites of Manganese where determined in the Crystal Structure of the Bacillus Subtilis Superoxide Dismutase, PDB code: 2rcv:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 2rcv

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Manganese binding site 1 out of 8 in the Crystal Structure of the Bacillus Subtilis Superoxide Dismutase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of the Bacillus Subtilis Superoxide Dismutase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn203

b:9.4
occ:1.00
OD2 A:ASP164 2.0 9.8 1.0
O A:HOH204 2.2 9.0 1.0
NE2 A:HIS168 2.2 9.2 1.0
NE2 A:HIS27 2.2 8.1 1.0
NE2 A:HIS82 2.3 10.7 1.0
CE1 A:HIS27 3.1 7.2 1.0
CG A:ASP164 3.1 8.8 1.0
CE1 A:HIS168 3.2 8.9 1.0
CD2 A:HIS168 3.2 9.7 1.0
CD2 A:HIS82 3.2 8.8 1.0
CE1 A:HIS82 3.2 12.6 1.0
CD2 A:HIS27 3.3 8.8 1.0
OD1 A:ASP164 3.5 9.6 1.0
ND1 A:HIS27 4.2 7.5 1.0
ND1 A:HIS168 4.3 8.5 1.0
ND1 A:HIS82 4.3 11.0 1.0
CG A:HIS168 4.3 8.3 1.0
CG A:HIS27 4.4 6.6 1.0
CG A:HIS82 4.4 8.0 1.0
CB A:ASP164 4.4 8.1 1.0
CZ2 A:TRP131 4.4 10.0 1.0
CB A:TRP166 4.6 7.8 1.0
NE2 A:GLN149 4.7 12.3 1.0
CG A:TRP166 4.8 8.2 1.0
CB A:ALA169 4.9 11.2 1.0

Manganese binding site 2 out of 8 in 2rcv

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Manganese binding site 2 out of 8 in the Crystal Structure of the Bacillus Subtilis Superoxide Dismutase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of the Bacillus Subtilis Superoxide Dismutase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn203

b:10.1
occ:1.00
OD2 B:ASP164 2.0 10.5 1.0
NE2 B:HIS168 2.2 10.5 1.0
NE2 B:HIS82 2.2 11.7 1.0
NE2 B:HIS27 2.2 10.9 1.0
O B:HOH205 2.3 10.6 1.0
CG B:ASP164 3.1 9.9 1.0
CE1 B:HIS168 3.2 8.9 1.0
CE1 B:HIS27 3.2 9.2 1.0
CE1 B:HIS82 3.2 13.6 1.0
CD2 B:HIS82 3.2 13.2 1.0
CD2 B:HIS168 3.2 10.1 1.0
CD2 B:HIS27 3.3 9.7 1.0
OD1 B:ASP164 3.5 9.1 1.0
ND1 B:HIS27 4.3 8.3 1.0
ND1 B:HIS168 4.3 9.3 1.0
ND1 B:HIS82 4.3 12.4 1.0
CB B:ASP164 4.4 8.9 1.0
CG B:HIS82 4.4 11.8 1.0
CG B:HIS27 4.4 9.7 1.0
CG B:HIS168 4.4 8.8 1.0
CZ2 B:TRP131 4.5 10.4 1.0
CB B:TRP166 4.6 9.5 1.0
NE2 B:GLN149 4.7 10.7 1.0
CG B:TRP166 4.7 7.7 1.0
CB B:ALA169 5.0 8.0 1.0

Manganese binding site 3 out of 8 in 2rcv

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Manganese binding site 3 out of 8 in the Crystal Structure of the Bacillus Subtilis Superoxide Dismutase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of the Bacillus Subtilis Superoxide Dismutase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn203

b:10.7
occ:1.00
OD2 C:ASP164 2.0 13.0 1.0
O C:HOH204 2.1 13.7 1.0
NE2 C:HIS27 2.2 11.3 1.0
NE2 C:HIS82 2.3 14.7 1.0
NE2 C:HIS168 2.3 11.7 1.0
CG C:ASP164 3.1 12.5 1.0
CE1 C:HIS27 3.1 9.4 1.0
CE1 C:HIS82 3.2 14.0 1.0
CD2 C:HIS27 3.2 10.6 1.0
CE1 C:HIS168 3.2 9.3 1.0
CD2 C:HIS82 3.3 14.0 1.0
CD2 C:HIS168 3.3 11.3 1.0
OD1 C:ASP164 3.5 11.8 1.0
ND1 C:HIS27 4.2 11.8 1.0
ND1 C:HIS82 4.3 12.3 1.0
CG C:HIS27 4.3 10.7 1.0
ND1 C:HIS168 4.4 9.7 1.0
CB C:ASP164 4.4 13.4 1.0
CG C:HIS82 4.4 13.0 1.0
CG C:HIS168 4.4 10.0 1.0
CZ2 C:TRP131 4.5 12.8 1.0
CB C:TRP166 4.6 10.1 1.0
NE2 C:GLN149 4.7 11.8 1.0
CG C:TRP166 4.8 9.9 1.0
CB C:ALA169 4.8 11.0 1.0

Manganese binding site 4 out of 8 in 2rcv

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Manganese binding site 4 out of 8 in the Crystal Structure of the Bacillus Subtilis Superoxide Dismutase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structure of the Bacillus Subtilis Superoxide Dismutase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn203

b:10.0
occ:1.00
OD2 D:ASP164 2.1 10.8 1.0
NE2 D:HIS168 2.2 10.9 1.0
NE2 D:HIS82 2.2 10.8 1.0
NE2 D:HIS27 2.2 9.9 1.0
O D:HOH212 2.4 14.9 1.0
CG D:ASP164 3.1 10.4 1.0
CD2 D:HIS82 3.1 13.1 1.0
CE1 D:HIS168 3.2 10.2 1.0
CE1 D:HIS27 3.2 10.5 1.0
CD2 D:HIS168 3.2 10.1 1.0
CE1 D:HIS82 3.2 15.0 1.0
CD2 D:HIS27 3.2 8.9 1.0
OD1 D:ASP164 3.5 11.2 1.0
ND1 D:HIS168 4.3 9.2 1.0
ND1 D:HIS27 4.3 10.5 1.0
ND1 D:HIS82 4.3 13.6 1.0
CG D:HIS82 4.3 12.8 1.0
CG D:HIS168 4.3 10.1 1.0
CG D:HIS27 4.4 10.9 1.0
CB D:ASP164 4.4 9.0 1.0
CZ2 D:TRP131 4.5 11.0 1.0
CB D:TRP166 4.6 10.8 1.0
NE2 D:GLN149 4.7 12.5 1.0
CG D:TRP166 4.8 12.1 1.0
CB D:ALA169 4.9 9.6 1.0

Manganese binding site 5 out of 8 in 2rcv

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Manganese binding site 5 out of 8 in the Crystal Structure of the Bacillus Subtilis Superoxide Dismutase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Crystal Structure of the Bacillus Subtilis Superoxide Dismutase within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mn203

b:8.9
occ:1.00
OD2 E:ASP164 2.0 11.6 1.0
O E:HOH209 2.2 13.7 1.0
NE2 E:HIS27 2.2 9.3 1.0
NE2 E:HIS82 2.2 9.8 1.0
NE2 E:HIS168 2.2 8.8 1.0
CG E:ASP164 3.1 10.2 1.0
CE1 E:HIS27 3.1 10.0 1.0
CE1 E:HIS168 3.2 8.2 1.0
CD2 E:HIS82 3.2 9.1 1.0
CE1 E:HIS82 3.2 10.2 1.0
CD2 E:HIS27 3.2 9.3 1.0
CD2 E:HIS168 3.2 7.8 1.0
OD1 E:ASP164 3.5 11.1 1.0
ND1 E:HIS27 4.3 10.1 1.0
ND1 E:HIS168 4.3 7.3 1.0
ND1 E:HIS82 4.3 11.3 1.0
CB E:ASP164 4.3 9.0 1.0
CG E:HIS27 4.3 8.8 1.0
CG E:HIS82 4.4 10.3 1.0
CG E:HIS168 4.4 7.5 1.0
CZ2 E:TRP131 4.4 11.2 1.0
CB E:TRP166 4.6 8.7 1.0
NE2 E:GLN149 4.7 13.0 1.0
CG E:TRP166 4.8 7.6 1.0
CB E:ALA169 5.0 8.1 1.0

Manganese binding site 6 out of 8 in 2rcv

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Manganese binding site 6 out of 8 in the Crystal Structure of the Bacillus Subtilis Superoxide Dismutase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Crystal Structure of the Bacillus Subtilis Superoxide Dismutase within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mn203

b:9.4
occ:1.00
OD2 F:ASP164 2.1 11.2 1.0
NE2 F:HIS82 2.2 8.6 1.0
NE2 F:HIS27 2.2 7.4 1.0
NE2 F:HIS168 2.2 8.7 1.0
O F:HOH209 2.3 14.0 1.0
CG F:ASP164 3.1 7.7 1.0
CD2 F:HIS82 3.1 11.2 1.0
CE1 F:HIS27 3.1 8.0 1.0
CE1 F:HIS82 3.2 12.9 1.0
CE1 F:HIS168 3.2 10.5 1.0
CD2 F:HIS27 3.2 8.1 1.0
CD2 F:HIS168 3.2 11.2 1.0
OD1 F:ASP164 3.5 9.2 1.0
ND1 F:HIS82 4.3 8.7 1.0
ND1 F:HIS27 4.3 8.3 1.0
CG F:HIS82 4.3 11.4 1.0
ND1 F:HIS168 4.3 9.8 1.0
CB F:ASP164 4.4 7.8 1.0
CG F:HIS27 4.4 7.9 1.0
CG F:HIS168 4.4 7.3 1.0
CZ2 F:TRP131 4.5 9.8 1.0
NE2 F:GLN149 4.7 11.4 1.0
CB F:TRP166 4.7 9.0 1.0
CG F:TRP166 4.8 9.0 1.0
CB F:ALA169 5.0 10.4 1.0

Manganese binding site 7 out of 8 in 2rcv

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Manganese binding site 7 out of 8 in the Crystal Structure of the Bacillus Subtilis Superoxide Dismutase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Crystal Structure of the Bacillus Subtilis Superoxide Dismutase within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mn203

b:8.9
occ:1.00
OD2 G:ASP164 2.0 9.0 1.0
NE2 G:HIS27 2.1 5.4 1.0
NE2 G:HIS82 2.2 10.8 1.0
O G:HOH207 2.2 10.2 1.0
NE2 G:HIS168 2.2 8.3 1.0
CE1 G:HIS27 3.0 7.8 1.0
CG G:ASP164 3.1 11.7 1.0
CE1 G:HIS82 3.2 10.1 1.0
CD2 G:HIS82 3.2 9.9 1.0
CD2 G:HIS27 3.2 9.2 1.0
CD2 G:HIS168 3.2 6.7 1.0
CE1 G:HIS168 3.2 8.2 1.0
OD1 G:ASP164 3.6 9.8 1.0
ND1 G:HIS27 4.2 9.0 1.0
CG G:HIS27 4.3 7.5 1.0
ND1 G:HIS82 4.3 9.6 1.0
ND1 G:HIS168 4.3 8.5 1.0
CG G:HIS82 4.3 10.2 1.0
CB G:ASP164 4.3 9.6 1.0
CG G:HIS168 4.4 8.1 1.0
CZ2 G:TRP131 4.5 12.3 1.0
NE2 G:GLN149 4.6 12.1 1.0
CB G:TRP166 4.6 8.3 1.0
CG G:TRP166 4.8 8.5 1.0
CB G:ALA169 4.9 9.6 1.0

Manganese binding site 8 out of 8 in 2rcv

Go back to Manganese Binding Sites List in 2rcv
Manganese binding site 8 out of 8 in the Crystal Structure of the Bacillus Subtilis Superoxide Dismutase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Crystal Structure of the Bacillus Subtilis Superoxide Dismutase within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mn203

b:10.2
occ:1.00
OD2 H:ASP164 2.0 8.4 1.0
O H:HOH204 2.2 12.1 1.0
NE2 H:HIS82 2.2 7.0 1.0
NE2 H:HIS168 2.2 9.0 1.0
NE2 H:HIS27 2.3 8.8 1.0
CG H:ASP164 3.1 8.4 1.0
CE1 H:HIS82 3.2 11.2 1.0
CE1 H:HIS27 3.2 9.3 1.0
CE1 H:HIS168 3.2 8.2 1.0
CD2 H:HIS82 3.2 9.7 1.0
CD2 H:HIS168 3.3 9.8 1.0
CD2 H:HIS27 3.3 7.7 1.0
OD1 H:ASP164 3.5 9.2 1.0
ND1 H:HIS82 4.3 7.9 1.0
ND1 H:HIS27 4.3 7.4 1.0
ND1 H:HIS168 4.3 8.5 1.0
CB H:ASP164 4.3 6.7 1.0
CG H:HIS82 4.4 8.8 1.0
CG H:HIS27 4.4 8.7 1.0
CG H:HIS168 4.4 7.0 1.0
CZ2 H:TRP131 4.5 9.5 1.0
CB H:TRP166 4.6 9.3 1.0
NE2 H:GLN149 4.7 12.4 1.0
CG H:TRP166 4.8 7.1 1.0

Reference:

P.Liu, H.E.Ewis, Y.J.Huang, C.D.Lu, P.C.Tai, I.T.Weber. Structure of Bacillus Subtilis Superoxide Dismutase. Acta Crystallogr.,Sect.F V. 63 1003 2007.
ISSN: ESSN 1744-3091
PubMed: 18084079
DOI: 10.1107/S1744309107054127
Page generated: Sat Oct 5 15:07:48 2024

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