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Manganese in PDB 4g3h: Crystal Structure of Helicobacter Pylori Arginase

Protein crystallography data

The structure of Crystal Structure of Helicobacter Pylori Arginase, PDB code: 4g3h was solved by J.Zhang, X.Zhang, D.Li, Y.Hu, Q.Zou, D.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.90 / 2.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 94.690, 102.240, 148.610, 90.00, 90.00, 90.00
R / Rfree (%) 21.8 / 23

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of Helicobacter Pylori Arginase (pdb code 4g3h). 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 Helicobacter Pylori Arginase, PDB code: 4g3h:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 4g3h

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Manganese binding site 1 out of 8 in the Crystal Structure of Helicobacter Pylori Arginase


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 Helicobacter Pylori Arginase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn500

b:32.2
occ:1.00
 OD2 A:ASP116 2.1 18.3 1.0
OD2 A:ASP120 2.3 23.8 1.0
CD2 A:HIS91 2.3 16.6 1.0
OD2 A:ASP234 2.5 20.9 1.0
O A:HOH741 2.7 42.5 1.0
MN A:MN501 2.9 28.3 1.0
CG A:HIS91 3.0 18.5 1.0
CG A:ASP116 3.1 17.8 1.0
CG A:ASP120 3.2 25.2 1.0
OD1 A:ASP120 3.3 27.0 1.0
CB A:HIS91 3.3 17.8 1.0
OD1 A:ASP116 3.4 22.2 1.0
NE2 A:HIS91 3.5 19.8 1.0
CG A:ASP234 3.6 21.6 1.0
CB A:ASP234 4.0 18.0 1.0
OH A:TYR114 4.0 17.5 1.0
ND1 A:HIS91 4.3 20.5 1.0
CB A:ASP116 4.4 17.4 1.0
CE1 A:HIS91 4.4 18.8 1.0
CE2 A:TYR114 4.6 19.7 1.0
CB A:ASP120 4.6 24.0 1.0
CZ A:TYR114 4.6 18.6 1.0
OD1 A:ASP234 4.7 22.2 1.0
ND1 A:HIS118 4.7 25.8 1.0
O A:HOH661 4.7 30.8 1.0
OD2 A:ASP236 4.8 25.5 1.0
CB A:HIS118 4.9 25.1 1.0
CA A:HIS91 4.9 20.3 1.0
CG A:GLU281 4.9 25.1 1.0

Manganese binding site 2 out of 8 in 4g3h

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Manganese binding site 2 out of 8 in the Crystal Structure of Helicobacter Pylori Arginase


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 Helicobacter Pylori Arginase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn501

b:28.3
occ:1.00
 OD2 A:ASP236 2.1 25.5 1.0
OD1 A:ASP116 2.2 22.2 1.0
ND1 A:HIS118 2.3 25.8 1.0
OD2 A:ASP234 2.3 20.9 1.0
O A:HOH741 2.7 42.5 1.0
CG A:ASP236 2.9 24.4 1.0
MN A:MN500 2.9 32.2 1.0
OD1 A:ASP236 2.9 27.5 1.0
CG A:ASP116 3.1 17.8 1.0
CE1 A:HIS118 3.1 25.0 1.0
CG A:ASP234 3.1 21.6 1.0
OD2 A:ASP116 3.2 18.3 1.0
CG A:HIS118 3.4 26.0 1.0
OD1 A:ASP234 3.7 22.2 1.0
CB A:HIS118 3.9 25.1 1.0
N A:HIS118 4.0 20.7 1.0
CB A:ASP234 4.1 18.0 1.0
N A:ALA117 4.2 21.2 1.0
CB A:ASP236 4.3 23.1 1.0
NE2 A:HIS118 4.3 28.3 1.0
O A:HOH696 4.5 27.6 1.0
CB A:ASP116 4.5 17.4 1.0
CD2 A:HIS118 4.5 27.1 1.0
CA A:HIS118 4.5 21.4 1.0
OD1 A:ASP120 4.6 27.0 1.0
OD2 A:ASP120 4.7 23.8 1.0
CB A:ALA117 4.8 23.9 1.0
C A:ALA117 4.8 23.8 1.0
CD2 A:HIS91 4.9 16.6 1.0
CA A:ALA117 4.9 22.9 1.0
CA A:ASP116 4.9 22.2 1.0

Manganese binding site 3 out of 8 in 4g3h

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Manganese binding site 3 out of 8 in the Crystal Structure of Helicobacter Pylori Arginase


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 Helicobacter Pylori Arginase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn500

b:41.0
occ:1.00
 OD2 B:ASP116 2.1 20.3 1.0
OD2 B:ASP120 2.3 23.0 1.0
CD2 B:HIS91 2.3 23.2 1.0
OD2 B:ASP234 2.4 23.1 1.0
O B:HOH699 2.8 57.8 1.0
MN B:MN501 2.9 26.9 1.0
CG B:HIS91 3.1 23.8 1.0
CG B:ASP116 3.1 19.4 1.0
CG B:ASP120 3.2 22.8 1.0
CB B:HIS91 3.3 21.5 1.0
OD1 B:ASP116 3.4 19.4 1.0
OD1 B:ASP120 3.4 21.9 1.0
NE2 B:HIS91 3.5 23.3 1.0
CG B:ASP234 3.5 23.2 1.0
CB B:ASP234 4.0 23.8 1.0
OH B:TYR114 4.0 21.9 1.0
ND1 B:HIS91 4.3 26.8 1.0
O B:HOH712 4.3 47.3 1.0
CB B:ASP116 4.4 19.7 1.0
CE1 B:HIS91 4.5 24.3 1.0
OD1 B:ASP234 4.6 23.1 1.0
CB B:ASP120 4.6 20.1 1.0
CE2 B:TYR114 4.6 19.1 1.0
ND1 B:HIS118 4.6 23.7 1.0
CZ B:TYR114 4.7 20.3 1.0
OD2 B:ASP236 4.7 25.4 1.0
CG B:GLU281 4.8 26.2 1.0
CB B:HIS118 4.8 20.0 1.0
CA B:HIS91 4.9 21.9 1.0

Manganese binding site 4 out of 8 in 4g3h

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Manganese binding site 4 out of 8 in the Crystal Structure of Helicobacter Pylori Arginase


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 Helicobacter Pylori Arginase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn501

b:26.9
occ:1.00
 OD2 B:ASP236 2.1 25.4 1.0
OD1 B:ASP116 2.2 19.4 1.0
OD2 B:ASP234 2.3 23.1 1.0
ND1 B:HIS118 2.3 23.7 1.0
CG B:ASP236 2.9 23.1 1.0
MN B:MN500 2.9 41.0 1.0
OD1 B:ASP236 2.9 21.7 1.0
O B:HOH699 3.0 57.8 1.0
CG B:ASP116 3.0 19.4 1.0
CE1 B:HIS118 3.1 24.4 1.0
CG B:ASP234 3.1 23.2 1.0
OD2 B:ASP116 3.2 20.3 1.0
CG B:HIS118 3.4 20.8 1.0
OD1 B:ASP234 3.7 23.1 1.0
CB B:HIS118 3.8 20.0 1.0
N B:HIS118 4.0 16.0 1.0
CB B:ASP234 4.1 23.8 1.0
N B:ALA117 4.2 18.5 1.0
NE2 B:HIS118 4.3 25.6 1.0
CB B:ASP236 4.3 21.0 1.0
CB B:ASP116 4.4 19.7 1.0
CD2 B:HIS118 4.5 23.1 1.0
CA B:HIS118 4.5 17.3 1.0
OD1 B:ASP120 4.6 21.9 1.0
O B:HOH631 4.6 29.9 1.0
OD2 B:ASP120 4.7 23.0 1.0
CB B:ALA117 4.7 16.2 1.0
C B:ALA117 4.8 17.9 1.0
CA B:ALA117 4.8 20.1 1.0
CA B:ASP116 4.9 18.3 1.0
CD2 B:HIS91 4.9 23.2 1.0
C B:ASP116 5.0 18.8 1.0

Manganese binding site 5 out of 8 in 4g3h

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Manganese binding site 5 out of 8 in the Crystal Structure of Helicobacter Pylori Arginase


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 Helicobacter Pylori Arginase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn500

b:37.8
occ:1.00
 OD2 C:ASP116 2.1 20.8 1.0
OD2 C:ASP120 2.2 24.9 1.0
CD2 C:HIS91 2.3 21.5 1.0
O C:HOH746 2.5 42.7 1.0
OD2 C:ASP234 2.6 24.6 1.0
MN C:MN501 3.0 25.6 1.0
CG C:HIS91 3.1 21.7 1.0
CG C:ASP116 3.1 19.1 1.0
CG C:ASP120 3.1 24.6 1.0
OD1 C:ASP120 3.3 24.6 1.0
CB C:HIS91 3.4 18.8 1.0
OD1 C:ASP116 3.4 16.7 1.0
NE2 C:HIS91 3.5 21.2 1.0
CG C:ASP234 3.6 25.0 1.0
OH C:TYR114 4.0 15.2 1.0
CB C:ASP234 4.0 20.3 1.0
ND1 C:HIS91 4.3 23.5 1.0
O C:HOH722 4.4 41.8 1.0
CB C:ASP116 4.4 20.1 1.0
CE1 C:HIS91 4.5 22.3 1.0
CB C:ASP120 4.5 23.2 1.0
CE2 C:TYR114 4.6 14.9 1.0
ND1 C:HIS118 4.7 20.6 1.0
CZ C:TYR114 4.7 14.8 1.0
OD1 C:ASP234 4.7 23.0 1.0
CB C:HIS118 4.8 18.0 1.0
OD2 C:ASP236 4.8 22.4 1.0
CG C:GLU281 4.9 22.3 1.0
CA C:HIS91 4.9 22.6 1.0
O C:HOH705 5.0 42.4 1.0

Manganese binding site 6 out of 8 in 4g3h

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Manganese binding site 6 out of 8 in the Crystal Structure of Helicobacter Pylori Arginase


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 Helicobacter Pylori Arginase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn501

b:25.6
occ:1.00
 OD2 C:ASP236 2.1 22.4 1.0
OD1 C:ASP116 2.2 16.7 1.0
ND1 C:HIS118 2.3 20.6 1.0
OD2 C:ASP234 2.4 24.6 1.0
CG C:ASP236 2.9 21.3 1.0
O C:HOH746 2.9 42.7 1.0
MN C:MN500 3.0 37.8 1.0
OD1 C:ASP236 3.0 23.1 1.0
CG C:ASP116 3.0 19.1 1.0
CE1 C:HIS118 3.1 22.8 1.0
CG C:ASP234 3.1 25.0 1.0
OD2 C:ASP116 3.2 20.8 1.0
CG C:HIS118 3.4 19.2 1.0
OD1 C:ASP234 3.7 23.0 1.0
CB C:HIS118 3.8 18.0 1.0
N C:HIS118 4.0 13.3 1.0
CB C:ASP234 4.0 20.3 1.0
N C:ALA117 4.2 14.6 1.0
NE2 C:HIS118 4.3 22.9 1.0
CB C:ASP236 4.3 21.2 1.0
CB C:ASP116 4.4 20.1 1.0
CD2 C:HIS118 4.4 20.6 1.0
CA C:HIS118 4.5 15.4 1.0
OD1 C:ASP120 4.6 24.6 1.0
O C:HOH630 4.6 20.1 1.0
O C:HOH705 4.7 42.4 1.0
OD2 C:ASP120 4.7 24.9 1.0
C C:ALA117 4.8 15.1 1.0
CB C:ALA117 4.8 14.1 1.0
CA C:ASP116 4.9 15.1 1.0
CA C:ALA117 4.9 17.5 1.0
CD2 C:HIS91 4.9 21.5 1.0
C C:ASP116 5.0 15.8 1.0

Manganese binding site 7 out of 8 in 4g3h

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Manganese binding site 7 out of 8 in the Crystal Structure of Helicobacter Pylori Arginase


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 Helicobacter Pylori Arginase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn500

b:34.5
occ:1.00
 OD2 D:ASP116 2.0 18.8 1.0
CD2 D:HIS91 2.3 20.2 1.0
OD2 D:ASP120 2.3 24.0 1.0
OD2 D:ASP234 2.6 18.4 1.0
O D:HOH757 2.6 45.4 1.0
MN D:MN501 3.0 24.6 1.0
CG D:ASP116 3.0 17.8 1.0
CG D:HIS91 3.0 20.1 1.0
CG D:ASP120 3.2 23.9 1.0
OD1 D:ASP116 3.3 19.6 1.0
OD1 D:ASP120 3.3 25.7 1.0
CB D:HIS91 3.4 19.0 1.0
NE2 D:HIS91 3.4 20.9 1.0
CG D:ASP234 3.6 20.0 1.0
CB D:ASP234 3.9 16.3 1.0
OH D:TYR114 3.9 18.0 1.0
ND1 D:HIS91 4.3 23.6 1.0
CB D:ASP116 4.3 16.6 1.0
CE1 D:HIS91 4.4 21.8 1.0
CE2 D:TYR114 4.5 19.7 1.0
CZ D:TYR114 4.6 18.9 1.0
CB D:ASP120 4.6 21.9 1.0
ND1 D:HIS118 4.7 26.3 1.0
OD1 D:ASP234 4.7 17.9 1.0
OD2 D:ASP236 4.8 22.1 1.0
CB D:HIS118 4.8 25.7 1.0
O D:HOH618 4.9 32.5 1.0
CA D:HIS91 4.9 19.6 1.0
CG D:GLU281 5.0 21.7 1.0

Manganese binding site 8 out of 8 in 4g3h

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Manganese binding site 8 out of 8 in the Crystal Structure of Helicobacter Pylori Arginase


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 Helicobacter Pylori Arginase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn501

b:24.6
occ:1.00
 OD2 D:ASP236 2.2 22.1 1.0
OD1 D:ASP116 2.2 19.6 1.0
ND1 D:HIS118 2.3 26.3 1.0
OD2 D:ASP234 2.4 18.4 1.0
O D:HOH757 2.5 45.4 1.0
OD1 D:ASP236 2.8 23.7 1.0
CG D:ASP236 2.8 20.5 1.0
MN D:MN500 3.0 34.5 1.0
CG D:ASP116 3.1 17.8 1.0
CE1 D:HIS118 3.1 26.1 1.0
CG D:ASP234 3.1 20.0 1.0
OD2 D:ASP116 3.3 18.8 1.0
CG D:HIS118 3.4 25.9 1.0
OD1 D:ASP234 3.7 17.9 1.0
CB D:HIS118 3.9 25.7 1.0
N D:HIS118 4.0 22.3 1.0
CB D:ASP234 4.1 16.3 1.0
N D:ALA117 4.2 17.8 1.0
NE2 D:HIS118 4.3 29.1 1.0
CB D:ASP236 4.3 20.0 1.0
O D:HOH603 4.4 26.8 1.0
CB D:ASP116 4.5 16.6 1.0
CD2 D:HIS118 4.5 27.4 1.0
OD1 D:ASP120 4.6 25.7 1.0
CA D:HIS118 4.6 23.3 1.0
CB D:ALA117 4.8 22.0 1.0
OD2 D:ASP120 4.8 24.0 1.0
C D:ALA117 4.8 19.9 1.0
CA D:ALA117 4.9 18.9 1.0
CA D:ASP116 4.9 22.1 1.0
CD2 D:HIS91 4.9 20.2 1.0
C D:ASP116 5.0 22.9 1.0

Reference:

J.Zhang, X.Zhang, D.Li, Y.Hu, Q.Zou, D.Wang. Structure and Function Studies on Helicobacter Pylori Arginase To Be Published.
Page generated: Sat Oct 5 19:28:38 2024

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