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Zinc in PDB 2rcc: Crystal Structure of Putative Class I Ribonucleotide Reductase (NP_241368.1) From Bacillus Halodurans at 1.90 A Resolution

Enzymatic activity of Crystal Structure of Putative Class I Ribonucleotide Reductase (NP_241368.1) From Bacillus Halodurans at 1.90 A Resolution

All present enzymatic activity of Crystal Structure of Putative Class I Ribonucleotide Reductase (NP_241368.1) From Bacillus Halodurans at 1.90 A Resolution:
1.17.4.1;

Protein crystallography data

The structure of Crystal Structure of Putative Class I Ribonucleotide Reductase (NP_241368.1) From Bacillus Halodurans at 1.90 A Resolution, PDB code: 2rcc was solved by Joint Center For Structural Genomics (Jcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.50 / 1.90
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 175.260, 72.780, 111.770, 90.00, 124.90, 90.00
R / Rfree (%) 18.3 / 21.5

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Putative Class I Ribonucleotide Reductase (NP_241368.1) From Bacillus Halodurans at 1.90 A Resolution (pdb code 2rcc). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Putative Class I Ribonucleotide Reductase (NP_241368.1) From Bacillus Halodurans at 1.90 A Resolution, PDB code: 2rcc:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 2rcc

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Zinc binding site 1 out of 4 in the Crystal Structure of Putative Class I Ribonucleotide Reductase (NP_241368.1) From Bacillus Halodurans at 1.90 A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Putative Class I Ribonucleotide Reductase (NP_241368.1) From Bacillus Halodurans at 1.90 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn400

b:39.0
occ:0.70
O B:HOH498 2.1 44.5 1.0
ND1 B:HIS121 2.1 17.4 1.0
O B:HOH499 2.2 27.2 1.0
OE1 B:GLU118 2.2 31.0 1.0
OD1 B:ASP88 2.7 22.2 1.0
OD2 B:ASP88 2.8 35.1 1.0
CG B:ASP88 3.0 20.6 1.0
O B:HOH497 3.0 28.0 1.0
CE1 B:HIS121 3.1 19.0 1.0
CG B:HIS121 3.2 13.4 1.0
CD B:GLU118 3.3 24.3 1.0
ZN B:ZN401 3.4 27.8 0.7
CB B:HIS121 3.5 12.5 1.0
OE2 B:GLU118 3.6 30.2 1.0
OE2 B:GLU219 3.8 41.1 1.0
NE2 B:HIS121 4.2 18.5 1.0
CD2 B:HIS121 4.3 15.2 1.0
OE1 B:GLU219 4.3 35.1 1.0
CD B:GLU219 4.4 34.3 1.0
CB B:ASP88 4.4 18.8 1.0
CG2 B:ILE215 4.4 13.5 1.0
CZ B:PHE189 4.5 23.6 1.0
CE1 B:HIS222 4.6 13.9 1.0
CG B:GLU118 4.6 14.4 1.0
CE2 B:PHE189 4.6 21.5 1.0
CA B:GLU118 4.6 12.6 1.0
ND1 B:HIS222 4.7 16.3 1.0
CE1 B:PHE189 4.8 23.1 1.0
OH B:TYR125 4.9 29.3 1.0
CB B:GLU118 4.9 12.3 1.0

Zinc binding site 2 out of 4 in 2rcc

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Zinc binding site 2 out of 4 in the Crystal Structure of Putative Class I Ribonucleotide Reductase (NP_241368.1) From Bacillus Halodurans at 1.90 A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Putative Class I Ribonucleotide Reductase (NP_241368.1) From Bacillus Halodurans at 1.90 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:27.8
occ:0.70
OE2 B:GLU185 1.9 16.6 1.0
O B:HOH499 2.0 27.2 1.0
OE2 B:GLU118 2.1 30.2 1.0
OE1 B:GLU219 2.2 35.1 1.0
ND1 B:HIS222 2.3 16.3 1.0
O B:HOH497 2.3 28.0 1.0
CD B:GLU185 3.0 19.9 1.0
CD B:GLU118 3.0 24.3 1.0
CE1 B:HIS222 3.1 13.9 1.0
CD B:GLU219 3.2 34.3 1.0
OE1 B:GLU118 3.3 31.0 1.0
CG B:HIS222 3.4 19.7 1.0
ZN B:ZN400 3.4 39.0 0.7
CG B:GLU185 3.5 16.5 1.0
OE2 B:GLU219 3.5 41.1 1.0
CB B:HIS222 3.8 18.6 1.0
OE1 B:GLU185 4.0 26.5 1.0
CB B:GLU185 4.2 16.4 1.0
NE2 B:HIS222 4.3 14.2 1.0
CG B:GLU118 4.4 14.4 1.0
OD1 B:ASP88 4.5 22.2 1.0
CD2 B:HIS222 4.5 12.7 1.0
CG B:GLU219 4.5 28.4 1.0
O B:HOH498 4.5 44.5 1.0
CG B:GLN91 4.5 16.2 1.0
NE2 B:GLN91 4.7 21.5 1.0
CA B:GLU219 4.8 18.2 1.0
ND1 B:HIS121 4.8 17.4 1.0
CE1 B:HIS121 4.9 19.0 1.0
CA B:GLU185 5.0 18.3 1.0

Zinc binding site 3 out of 4 in 2rcc

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Zinc binding site 3 out of 4 in the Crystal Structure of Putative Class I Ribonucleotide Reductase (NP_241368.1) From Bacillus Halodurans at 1.90 A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Putative Class I Ribonucleotide Reductase (NP_241368.1) From Bacillus Halodurans at 1.90 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn400

b:53.0
occ:0.70
ND1 C:HIS121 2.0 11.2 1.0
OE1 C:GLU118 2.5 34.9 1.0
OD2 C:ASP88 2.6 55.4 1.0
OD1 C:ASP88 2.7 35.8 1.0
CE1 C:HIS121 2.9 8.9 1.0
CG C:ASP88 3.0 37.5 1.0
CG C:HIS121 3.0 9.2 1.0
O C:HOH502 3.4 36.3 1.0
CB C:HIS121 3.4 12.3 1.0
ZN C:ZN401 3.5 40.6 0.7
CD C:GLU118 3.6 29.7 1.0
OE2 C:GLU219 3.8 43.1 1.0
OE1 C:GLU219 3.9 40.3 1.0
NE2 C:HIS121 4.0 13.8 1.0
CG2 C:ILE215 4.1 12.3 1.0
CD2 C:HIS121 4.1 14.1 1.0
OE2 C:GLU118 4.2 39.1 1.0
CE2 C:PHE189 4.2 36.0 1.0
CD C:GLU219 4.2 42.9 1.0
CB C:ASP88 4.4 28.8 1.0
CZ C:PHE189 4.5 36.4 1.0
CA C:GLU118 4.6 8.4 1.0
CD2 C:PHE189 4.6 36.5 1.0
CE1 C:HIS222 4.7 13.6 1.0
CG C:GLU118 4.8 21.8 1.0
ND1 C:HIS222 4.9 22.0 1.0
CA C:HIS121 5.0 10.2 1.0

Zinc binding site 4 out of 4 in 2rcc

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Zinc binding site 4 out of 4 in the Crystal Structure of Putative Class I Ribonucleotide Reductase (NP_241368.1) From Bacillus Halodurans at 1.90 A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Putative Class I Ribonucleotide Reductase (NP_241368.1) From Bacillus Halodurans at 1.90 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:40.6
occ:0.70
OE2 C:GLU185 2.0 29.7 1.0
OE1 C:GLU219 2.1 40.3 1.0
ND1 C:HIS222 2.2 22.0 1.0
O C:HOH502 2.4 36.3 1.0
OE2 C:GLU118 2.4 39.1 1.0
CE1 C:HIS222 3.0 13.6 1.0
CD C:GLU185 3.0 29.6 1.0
OE1 C:GLU118 3.1 34.9 1.0
CD C:GLU118 3.1 29.7 1.0
CD C:GLU219 3.2 42.9 1.0
CG C:HIS222 3.3 20.1 1.0
ZN C:ZN400 3.5 53.0 0.7
CG C:GLU185 3.6 20.4 1.0
OE2 C:GLU219 3.7 43.1 1.0
CB C:HIS222 3.8 15.9 1.0
OE1 C:GLU185 4.0 42.8 1.0
CB C:GLU185 4.1 18.9 1.0
NE2 C:HIS222 4.2 18.5 1.0
OD1 C:ASP88 4.3 35.8 1.0
CD2 C:HIS222 4.3 17.1 1.0
CG C:GLU219 4.4 33.8 1.0
CA C:GLU219 4.5 19.0 1.0
CG C:GLN91 4.6 30.6 1.0
CG C:GLU118 4.6 21.8 1.0
ND1 C:HIS121 4.7 11.2 1.0
CE1 C:HIS121 4.7 8.9 1.0
CA C:GLU185 4.8 17.7 1.0
CB C:GLU219 4.9 26.4 1.0
NE2 C:GLN91 4.9 28.2 1.0
CD2 C:LEU114 5.0 26.4 1.0

Reference:

Joint Center For Structural Genomics (Jcsg), Joint Center For Structural Genomics (Jcsg). N/A N/A.
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