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Zinc in PDB 4col: Crystal Structure of the Anaerobic Ribonucleotide Reductase From Thermotoga Maritima with Datp Bound in the Specificity Site

Enzymatic activity of Crystal Structure of the Anaerobic Ribonucleotide Reductase From Thermotoga Maritima with Datp Bound in the Specificity Site

All present enzymatic activity of Crystal Structure of the Anaerobic Ribonucleotide Reductase From Thermotoga Maritima with Datp Bound in the Specificity Site:
1.17.4.2;

Protein crystallography data

The structure of Crystal Structure of the Anaerobic Ribonucleotide Reductase From Thermotoga Maritima with Datp Bound in the Specificity Site, PDB code: 4col was solved by O.Aurelius, R.Johansson, V.Bagenholm, T.Beck, A.Balhuizen, D.Lundin, B.M.Sjoberg, E.Mulliez, D.T.Logan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.136 / 1.96
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 78.000, 94.120, 86.710, 90.00, 112.03, 90.00
R / Rfree (%) 19.11 / 22.55

Other elements in 4col:

The structure of Crystal Structure of the Anaerobic Ribonucleotide Reductase From Thermotoga Maritima with Datp Bound in the Specificity Site also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the Anaerobic Ribonucleotide Reductase From Thermotoga Maritima with Datp Bound in the Specificity Site (pdb code 4col). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of the Anaerobic Ribonucleotide Reductase From Thermotoga Maritima with Datp Bound in the Specificity Site, PDB code: 4col:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 4col

Go back to Zinc Binding Sites List in 4col
Zinc binding site 1 out of 2 in the Crystal Structure of the Anaerobic Ribonucleotide Reductase From Thermotoga Maritima with Datp Bound in the Specificity Site


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 the Anaerobic Ribonucleotide Reductase From Thermotoga Maritima with Datp Bound in the Specificity Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn700

b:60.2
occ:1.00
 ND1 A:HIS598 2.0 48.5 1.0
SG A:CYS594 2.3 54.0 1.0
SG A:CYS605 2.3 56.8 1.0
SG A:CYS608 2.4 60.9 1.0
CE1 A:HIS598 2.9 53.5 1.0
CG A:HIS598 3.1 45.9 1.0
CB A:CYS608 3.2 67.4 1.0
CB A:CYS605 3.2 56.9 1.0
CB A:HIS598 3.5 47.1 1.0
CB A:CYS594 3.5 57.9 1.0
N A:CYS608 3.7 69.2 1.0
CA A:CYS608 4.0 67.6 1.0
NE2 A:HIS598 4.1 51.1 1.0
CD2 A:HIS598 4.2 49.6 1.0
CB A:VAL607 4.3 67.5 1.0
N A:HIS598 4.6 47.3 1.0
CA A:HIS598 4.6 45.1 1.0
CB A:ASP596 4.7 57.0 1.0
CA A:CYS605 4.7 58.9 1.0
CG1 A:VAL607 4.7 65.4 1.0
C A:VAL607 4.7 70.0 1.0
N A:GLY609 4.8 67.7 1.0
C A:CYS608 4.8 69.2 1.0
CA A:CYS594 4.8 58.2 1.0
CE1 A:PHE600 5.0 53.3 1.0
CA A:VAL607 5.0 68.1 1.0

Zinc binding site 2 out of 2 in 4col

Go back to Zinc Binding Sites List in 4col
Zinc binding site 2 out of 2 in the Crystal Structure of the Anaerobic Ribonucleotide Reductase From Thermotoga Maritima with Datp Bound in the Specificity Site


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 the Anaerobic Ribonucleotide Reductase From Thermotoga Maritima with Datp Bound in the Specificity Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn700

b:53.1
occ:1.00
 ND1 B:HIS598 2.0 47.8 1.0
SG B:CYS608 2.2 60.8 1.0
SG B:CYS594 2.3 54.1 1.0
SG B:CYS605 2.3 50.9 1.0
CE1 B:HIS598 3.0 49.9 1.0
CG B:HIS598 3.0 46.4 1.0
CB B:CYS605 3.3 61.7 1.0
CB B:HIS598 3.3 44.9 1.0
CB B:CYS608 3.4 60.9 1.0
CB B:CYS594 3.5 51.0 1.0
N B:CYS608 3.8 59.1 1.0
NE2 B:HIS598 4.1 49.0 1.0
CD2 B:HIS598 4.1 45.8 1.0
CA B:CYS608 4.2 60.2 1.0
CB B:VAL607 4.4 57.0 1.0
CA B:HIS598 4.5 44.5 1.0
N B:HIS598 4.5 45.0 1.0
CA B:CYS605 4.7 59.6 1.0
C B:CYS608 4.8 63.6 1.0
CB B:LYS610 4.8 61.1 1.0
CB B:ASP596 4.8 50.5 1.0
C B:VAL607 4.8 60.0 1.0
N B:GLY609 4.8 62.6 1.0
CA B:CYS594 4.9 52.2 1.0
N B:LYS610 4.9 60.3 1.0
CG1 B:VAL607 5.0 57.9 1.0
N B:VAL607 5.0 55.9 1.0
CA B:VAL607 5.0 58.3 1.0

Reference:

O.Aurelius, R.Johansson, V.Bagenholm, T.Beck, A.Balhuizen, D.Lundin, B.M.Sjoberg, E.Mulliez, D.T.Logan. The Crystal Structure of the Thermotoga Maritima Anaerobic Ribonucleotide Reductase Lacks A Radical Cysteine Pre-Positioned in the Active Site To Be Published.
Page generated: Sat Oct 26 20:56:13 2024

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