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Manganese in PDB 8dq5: X-Ray Crystal Structure of Flavobacterium Johnsoniae Dimanganese(II) Class Id Ribonucleotide Reductase T191I Variant

Enzymatic activity of X-Ray Crystal Structure of Flavobacterium Johnsoniae Dimanganese(II) Class Id Ribonucleotide Reductase T191I Variant

All present enzymatic activity of X-Ray Crystal Structure of Flavobacterium Johnsoniae Dimanganese(II) Class Id Ribonucleotide Reductase T191I Variant:
1.17.4.1;

Protein crystallography data

The structure of X-Ray Crystal Structure of Flavobacterium Johnsoniae Dimanganese(II) Class Id Ribonucleotide Reductase T191I Variant, PDB code: 8dq5 was solved by H.R.Rose, A.K.Boal, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.57 / 2.10
Space group P 31
Cell size a, b, c (Å), α, β, γ (°) 53.771, 53.771, 221.288, 90, 90, 120
R / Rfree (%) 24.7 / 28.2

Other elements in 8dq5:

The structure of X-Ray Crystal Structure of Flavobacterium Johnsoniae Dimanganese(II) Class Id Ribonucleotide Reductase T191I Variant also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Manganese Binding Sites:

The binding sites of Manganese atom in the X-Ray Crystal Structure of Flavobacterium Johnsoniae Dimanganese(II) Class Id Ribonucleotide Reductase T191I Variant (pdb code 8dq5). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the X-Ray Crystal Structure of Flavobacterium Johnsoniae Dimanganese(II) Class Id Ribonucleotide Reductase T191I Variant, PDB code: 8dq5:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 8dq5

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Manganese binding site 1 out of 4 in the X-Ray Crystal Structure of Flavobacterium Johnsoniae Dimanganese(II) Class Id Ribonucleotide Reductase T191I Variant


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of X-Ray Crystal Structure of Flavobacterium Johnsoniae Dimanganese(II) Class Id Ribonucleotide Reductase T191I Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn401

b:14.8
occ:0.30
 OE1 A:GLU67 2.3 19.9 1.0
O A:HOH535 2.5 11.8 1.0
ND1 A:HIS100 3.0 11.5 1.0
OE2 A:GLU195 3.3 21.9 1.0
CB A:HIS100 3.4 9.5 1.0
CD A:GLU67 3.4 18.8 1.0
O A:HOH508 3.5 9.4 1.0
CG A:HIS100 3.5 10.6 1.0
NZ A:LYS71 3.5 11.1 1.0
O A:HOH512 3.6 19.4 1.0
CG A:GLU97 3.8 17.8 1.0
CA A:GLU97 3.8 15.2 1.0
MN A:MN402 3.8 26.3 0.6
CB A:GLU97 4.0 11.0 1.0
OE2 A:GLU67 4.0 14.5 1.0
CE1 A:HIS100 4.1 13.9 1.0
O A:HOH502 4.2 13.9 1.0
O A:GLU97 4.3 10.9 1.0
CD A:GLU195 4.4 17.3 1.0
CG A:GLU67 4.4 9.8 1.0
C A:GLU97 4.6 11.5 1.0
CD A:LYS71 4.6 22.4 1.0
CB A:GLU67 4.6 11.1 1.0
CE A:LYS71 4.6 16.8 1.0
OE1 A:GLU195 4.7 20.7 1.0
CD2 A:HIS100 4.7 9.7 1.0
N A:GLU97 4.8 11.7 1.0
CA A:HIS100 4.8 12.5 1.0
CD A:GLU97 4.8 17.0 1.0
OE2 A:GLU97 4.9 17.8 1.0
O A:CYS96 5.0 7.0 1.0
NE2 A:HIS100 5.0 14.0 1.0

Manganese binding site 2 out of 4 in 8dq5

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Manganese binding site 2 out of 4 in the X-Ray Crystal Structure of Flavobacterium Johnsoniae Dimanganese(II) Class Id Ribonucleotide Reductase T191I Variant


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of X-Ray Crystal Structure of Flavobacterium Johnsoniae Dimanganese(II) Class Id Ribonucleotide Reductase T191I Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn402

b:26.3
occ:0.58
 OE2 A:GLU160 2.1 17.3 1.0
O A:HOH502 2.1 13.9 1.0
OE1 A:GLU195 2.3 20.7 1.0
O A:HOH512 2.3 19.4 1.0
ND1 A:HIS198 2.4 9.8 1.0
CD A:GLU195 3.0 17.3 1.0
OE2 A:GLU195 3.1 21.9 1.0
CD A:GLU160 3.2 12.6 1.0
CE1 A:HIS198 3.2 13.2 1.0
OE1 A:GLU160 3.5 15.0 1.0
CG A:HIS198 3.5 11.2 1.0
MN A:MN401 3.8 14.8 0.3
CB A:HIS198 3.9 6.1 1.0
NZ A:LYS71 3.9 11.1 1.0
OE2 A:GLU97 4.3 17.8 1.0
NE2 A:HIS198 4.4 11.1 1.0
CG A:GLU97 4.4 17.8 1.0
CG A:GLU195 4.4 9.0 1.0
OE1 A:GLU67 4.5 19.9 1.0
CG A:GLU160 4.5 21.8 1.0
CD2 A:HIS198 4.5 11.6 1.0
CA A:GLU195 4.6 8.9 1.0
CB A:GLU160 4.8 20.0 1.0
ND1 A:HIS100 4.8 11.5 1.0
CB A:GLU195 4.9 9.3 1.0
CD A:GLU97 4.9 17.0 1.0
CA A:GLU160 4.9 24.3 1.0
O A:ILE159 4.9 26.1 1.0
CE1 A:HIS100 5.0 13.9 1.0

Manganese binding site 3 out of 4 in 8dq5

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Manganese binding site 3 out of 4 in the X-Ray Crystal Structure of Flavobacterium Johnsoniae Dimanganese(II) Class Id Ribonucleotide Reductase T191I Variant


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of X-Ray Crystal Structure of Flavobacterium Johnsoniae Dimanganese(II) Class Id Ribonucleotide Reductase T191I Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn401

b:20.5
occ:0.31
 OE1 B:GLU67 2.5 20.2 1.0
O B:HOH507 3.1 10.2 1.0
NZ B:LYS71 3.1 13.3 1.0
CG B:GLU97 3.3 19.6 1.0
CD B:GLU67 3.3 24.8 1.0
MN B:MN402 3.3 38.8 0.7
O B:HOH504 3.3 26.2 1.0
OE2 B:GLU195 3.4 26.9 1.0
ND1 B:HIS100 3.5 14.9 1.0
OE2 B:GLU67 3.7 18.0 1.0
CB B:GLU97 3.7 10.8 1.0
O B:HOH501 3.8 18.3 1.0
CA B:GLU97 3.9 14.2 1.0
CB B:HIS100 4.0 11.3 1.0
CG B:HIS100 4.1 14.7 1.0
CE B:LYS71 4.2 24.6 1.0
CD B:LYS71 4.2 22.1 1.0
CD B:GLU97 4.3 18.4 1.0
OE2 B:GLU97 4.3 23.6 1.0
CG B:GLU67 4.4 12.3 1.0
CD B:GLU195 4.5 30.7 1.0
O B:GLU97 4.5 6.6 1.0
CE1 B:HIS100 4.6 19.2 1.0
CB B:GLU67 4.6 14.4 1.0
C B:GLU97 4.7 11.8 1.0
OE1 B:GLU195 4.8 38.6 1.0
N B:GLU97 4.9 8.4 1.0

Manganese binding site 4 out of 4 in 8dq5

Go back to Manganese Binding Sites List in 8dq5
Manganese binding site 4 out of 4 in the X-Ray Crystal Structure of Flavobacterium Johnsoniae Dimanganese(II) Class Id Ribonucleotide Reductase T191I Variant


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of X-Ray Crystal Structure of Flavobacterium Johnsoniae Dimanganese(II) Class Id Ribonucleotide Reductase T191I Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn402

b:38.8
occ:0.70
 O B:HOH504 2.0 26.2 1.0
OE2 B:GLU160 2.4 39.4 1.0
OE1 B:GLU195 2.6 38.6 1.0
ND1 B:HIS198 2.7 21.9 1.0
OE2 B:GLU195 2.8 26.9 1.0
CD B:GLU195 3.0 30.7 1.0
CD B:GLU160 3.2 44.1 1.0
OE1 B:GLU160 3.2 37.7 1.0
MN B:MN401 3.3 20.5 0.3
CE1 B:HIS198 3.5 20.9 1.0
CG B:HIS198 3.8 27.4 1.0
NZ B:LYS71 3.8 13.3 1.0
OE2 B:GLU97 4.0 23.6 1.0
CG B:GLU97 4.1 19.6 1.0
OE1 B:GLU67 4.1 20.2 1.0
CB B:HIS198 4.1 20.3 1.0
CG B:GLU195 4.5 21.9 1.0
CD B:GLU97 4.5 18.4 1.0
CG B:GLU160 4.7 45.0 1.0
NE2 B:HIS198 4.7 21.4 1.0
ND1 B:HIS100 4.8 14.9 1.0
CD2 B:HIS198 4.8 19.5 1.0
CA B:GLU195 4.9 20.6 1.0
CA B:GLU160 5.0 49.2 1.0
CD B:GLU67 5.0 24.8 1.0

Reference:

H.R.Rose, A.K.Boal. X-Ray Crystal Structure of Flavobacterium Johnsoniae Dimanganese(II) Class Id Ribonucleotide Reductase T191I Variant To Be Published.
Page generated: Sun Oct 6 11:33:37 2024

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