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Manganese in PDB 8dq4: X-Ray Crystal Structure of Flavobacterium Johnsoniae Dimanganese(II) Class Id Ribonucleotide Reductase Beta Subunit K71R Variant

Enzymatic activity of X-Ray Crystal Structure of Flavobacterium Johnsoniae Dimanganese(II) Class Id Ribonucleotide Reductase Beta Subunit K71R Variant

All present enzymatic activity of X-Ray Crystal Structure of Flavobacterium Johnsoniae Dimanganese(II) Class Id Ribonucleotide Reductase Beta Subunit K71R Variant:
1.17.4.1;

Protein crystallography data

The structure of X-Ray Crystal Structure of Flavobacterium Johnsoniae Dimanganese(II) Class Id Ribonucleotide Reductase Beta Subunit K71R Variant, PDB code: 8dq4 was solved by H.R.Rose, A.O.Maggiolo, J.J.Jung, A.K.Boal, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.84 / 2.35
Space group P 31
Cell size a, b, c (Å), α, β, γ (°) 53.551, 53.551, 220.947, 90, 90, 120
R / Rfree (%) 22.7 / 27.5

Manganese Binding Sites:

The binding sites of Manganese atom in the X-Ray Crystal Structure of Flavobacterium Johnsoniae Dimanganese(II) Class Id Ribonucleotide Reductase Beta Subunit K71R Variant (pdb code 8dq4). 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 Beta Subunit K71R Variant, PDB code: 8dq4:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 8dq4

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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 Beta Subunit K71R 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 Beta Subunit K71R Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn401

b:22.0
occ:1.00
 OE1 A:GLU195 2.0 20.1 1.0
OE2 A:GLU97 2.0 31.3 1.0
OE2 A:GLU160 2.0 25.5 1.0
ND1 A:HIS198 2.3 14.7 1.0
O A:HOH518 2.7 19.3 1.0
CD A:GLU160 2.8 18.3 1.0
OE1 A:GLU160 2.9 20.4 1.0
CD A:GLU97 3.0 27.6 1.0
CD A:GLU195 3.1 18.2 1.0
CE1 A:HIS198 3.2 16.7 1.0
OE1 A:GLU97 3.3 16.4 1.0
CG A:HIS198 3.4 16.8 1.0
MN A:MN402 3.5 14.8 1.0
OE2 A:GLU195 3.6 20.3 1.0
CB A:HIS198 3.8 14.7 1.0
CG A:GLU160 4.2 20.7 1.0
NE2 A:HIS198 4.4 12.9 1.0
CG A:GLU195 4.4 12.0 1.0
CG A:GLU97 4.4 19.1 1.0
CA A:GLU195 4.4 14.1 1.0
NH2 A:ARG71 4.4 28.7 1.0
CD2 A:HIS198 4.5 15.1 1.0
NE1 A:TRP74 4.5 15.6 1.0
CB A:GLU195 4.5 12.1 1.0
CB A:GLU160 4.8 14.8 1.0
CA A:GLU160 4.9 18.6 1.0
CD1 A:TRP74 4.9 12.6 1.0

Manganese binding site 2 out of 4 in 8dq4

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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 Beta Subunit K71R 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 Beta Subunit K71R Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn402

b:14.8
occ:1.00
 OE2 A:GLU195 2.0 20.3 1.0
OE1 A:GLU67 2.1 18.2 1.0
OE1 A:GLU97 2.1 16.4 1.0
ND1 A:HIS100 2.4 10.5 1.0
CD A:GLU67 2.8 18.1 1.0
OE2 A:GLU67 2.9 22.5 1.0
CD A:GLU195 2.9 18.2 1.0
CD A:GLU97 3.2 27.6 1.0
OE1 A:GLU195 3.2 20.1 1.0
O A:HOH518 3.3 19.3 1.0
CG A:HIS100 3.4 14.3 1.0
CE1 A:HIS100 3.4 16.4 1.0
MN A:MN401 3.5 22.0 1.0
CB A:HIS100 3.6 13.2 1.0
OE2 A:GLU97 3.6 31.3 1.0
NH1 A:ARG71 3.7 31.4 1.0
O A:HOH508 4.2 19.2 1.0
CG A:GLU67 4.3 17.2 1.0
CG A:GLU195 4.3 12.0 1.0
NE2 A:HIS100 4.5 14.2 1.0
CD2 A:HIS100 4.5 14.7 1.0
CG A:GLU97 4.5 19.1 1.0
CG2 A:THR191 4.6 12.4 1.0
CA A:GLU97 4.6 15.3 1.0
CZ A:ARG71 4.7 25.4 1.0
CB A:GLU97 4.8 14.3 1.0
NH2 A:ARG71 4.8 28.7 1.0
CE1 A:HIS198 4.8 16.7 1.0
ND1 A:HIS198 4.9 14.7 1.0

Manganese binding site 3 out of 4 in 8dq4

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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 Beta Subunit K71R 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 Beta Subunit K71R Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn401

b:28.8
occ:0.79
 OE2 B:GLU97 1.9 36.6 1.0
OE1 B:GLU195 2.1 31.6 1.0
OE2 B:GLU160 2.3 40.1 1.0
ND1 B:HIS198 2.4 28.1 1.0
O B:HOH512 2.5 30.2 1.0
CD B:GLU97 3.0 27.7 1.0
CD B:GLU160 3.1 35.7 1.0
OE1 B:GLU160 3.1 38.4 1.0
CD B:GLU195 3.2 32.5 1.0
CE1 B:HIS198 3.3 27.6 1.0
CG B:HIS198 3.4 28.6 1.0
OE1 B:GLU97 3.6 23.5 1.0
MN B:MN402 3.6 20.4 0.9
OE2 B:GLU195 3.7 38.6 1.0
CB B:HIS198 3.7 25.4 1.0
CG B:GLU97 4.2 20.8 1.0
CG B:GLU195 4.5 28.4 1.0
NE2 B:HIS198 4.5 29.1 1.0
CG B:GLU160 4.5 31.0 1.0
CD2 B:HIS198 4.5 29.3 1.0
CA B:GLU195 4.6 30.1 1.0
NH2 B:ARG71 4.6 30.3 1.0
NE1 B:TRP74 4.7 26.2 1.0
CB B:GLU195 4.7 31.2 1.0
ND1 B:HIS100 5.0 17.6 1.0

Manganese binding site 4 out of 4 in 8dq4

Go back to Manganese Binding Sites List in 8dq4
Manganese binding site 4 out of 4 in the X-Ray Crystal Structure of Flavobacterium Johnsoniae Dimanganese(II) Class Id Ribonucleotide Reductase Beta Subunit K71R 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 Beta Subunit K71R Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn402

b:20.4
occ:0.92
 ND1 B:HIS100 2.3 17.6 1.0
OE1 B:GLU97 2.3 23.5 1.0
OE2 B:GLU195 2.3 38.6 1.0
OE1 B:GLU67 2.3 29.4 1.0
OE2 B:GLU67 2.4 26.9 1.0
CD B:GLU67 2.7 23.8 1.0
CD B:GLU195 3.1 32.5 1.0
CD B:GLU97 3.1 27.7 1.0
OE2 B:GLU97 3.2 36.6 1.0
CE1 B:HIS100 3.2 21.9 1.0
CG B:HIS100 3.3 20.3 1.0
OE1 B:GLU195 3.4 31.6 1.0
O B:HOH512 3.4 30.2 1.0
CB B:HIS100 3.6 15.3 1.0
MN B:MN401 3.6 28.8 0.8
NH1 B:ARG71 4.0 31.0 1.0
CG B:GLU67 4.2 20.7 1.0
CG B:GLU195 4.3 28.4 1.0
O B:HOH515 4.4 19.8 1.0
NE2 B:HIS100 4.4 13.8 1.0
CD2 B:HIS100 4.5 17.7 1.0
CG B:GLU97 4.5 20.8 1.0
CG2 B:THR191 4.5 14.0 1.0
CA B:GLU97 4.8 17.2 1.0
CB B:GLU97 4.9 15.0 1.0
CB B:GLU67 5.0 17.2 1.0

Reference:

H.R.Rose, A.K.Boal. X-Ray Crystal Structure of Flavobacterium Johnsoniae Dimanganese(II) Class Id Ribonucleotide Reductase Beta Subunit K71R Variant To Be Published.
Page generated: Thu Dec 28 11:04:44 2023

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