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Zinc in PDB 5a89: Crystal Structure of the Riboflavin Kinase Module of Fad Synthetase From Corynebacterium Ammoniagenes in Complex with Fmn and Adp (P 21 21 21)

Enzymatic activity of Crystal Structure of the Riboflavin Kinase Module of Fad Synthetase From Corynebacterium Ammoniagenes in Complex with Fmn and Adp (P 21 21 21)

All present enzymatic activity of Crystal Structure of the Riboflavin Kinase Module of Fad Synthetase From Corynebacterium Ammoniagenes in Complex with Fmn and Adp (P 21 21 21):
2.7.1.26;

Protein crystallography data

The structure of Crystal Structure of the Riboflavin Kinase Module of Fad Synthetase From Corynebacterium Ammoniagenes in Complex with Fmn and Adp (P 21 21 21), PDB code: 5a89 was solved by B.Herguedas, M.Martinez-Julvez, J.A.Hermoso, M.Medina, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 57.62 / 1.65
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 43.400, 70.480, 100.080, 90.00, 90.00, 90.00
R / Rfree (%) 14.349 / 17.551

Other elements in 5a89:

The structure of Crystal Structure of the Riboflavin Kinase Module of Fad Synthetase From Corynebacterium Ammoniagenes in Complex with Fmn and Adp (P 21 21 21) 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 Riboflavin Kinase Module of Fad Synthetase From Corynebacterium Ammoniagenes in Complex with Fmn and Adp (P 21 21 21) (pdb code 5a89). 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 Riboflavin Kinase Module of Fad Synthetase From Corynebacterium Ammoniagenes in Complex with Fmn and Adp (P 21 21 21), PDB code: 5a89:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 5a89

Go back to Zinc Binding Sites List in 5a89
Zinc binding site 1 out of 2 in the Crystal Structure of the Riboflavin Kinase Module of Fad Synthetase From Corynebacterium Ammoniagenes in Complex with Fmn and Adp (P 21 21 21)


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 Riboflavin Kinase Module of Fad Synthetase From Corynebacterium Ammoniagenes in Complex with Fmn and Adp (P 21 21 21) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn343

b:12.9
occ:0.50
 OD1 A:ASP321 1.9 18.7 1.0
O A:HOH2004 2.0 25.8 1.0
NE2 A:HIS186 2.1 23.4 1.0
NE2 A:HIS325 2.1 27.2 1.0
CG A:ASP321 2.9 17.5 1.0
CD2 A:HIS325 2.9 26.5 1.0
CE1 A:HIS186 3.0 23.6 1.0
OD2 A:ASP321 3.1 17.6 1.0
CD2 A:HIS186 3.1 22.8 1.0
CE1 A:HIS325 3.3 28.1 1.0
O A:HOH2005 3.5 56.6 1.0
O A:HOH2168 3.8 31.5 1.0
CG1 A:VAL288 4.1 13.9 1.0
CG A:HIS325 4.1 26.9 1.0
O A:HOH2146 4.2 38.8 1.0
ND1 A:HIS186 4.2 22.6 1.0
CB A:ASP321 4.2 17.2 1.0
CG A:HIS186 4.3 22.8 1.0
ND1 A:HIS325 4.3 28.2 1.0
CA A:ASP321 4.8 18.2 1.0
CG2 A:VAL288 4.9 12.8 1.0
O A:ASP321 5.0 19.0 1.0

Zinc binding site 2 out of 2 in 5a89

Go back to Zinc Binding Sites List in 5a89
Zinc binding site 2 out of 2 in the Crystal Structure of the Riboflavin Kinase Module of Fad Synthetase From Corynebacterium Ammoniagenes in Complex with Fmn and Adp (P 21 21 21)


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 Riboflavin Kinase Module of Fad Synthetase From Corynebacterium Ammoniagenes in Complex with Fmn and Adp (P 21 21 21) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn343

b:18.9
occ:0.50
 O B:HOH2004 1.9 38.2 1.0
OD1 B:ASP321 2.0 16.1 1.0
NE2 B:HIS186 2.1 26.9 1.0
NE2 B:HIS325 2.2 39.0 1.0
CD2 B:HIS325 2.8 38.8 1.0
CG B:ASP321 2.9 15.5 1.0
CD2 B:HIS186 3.1 26.7 1.0
CE1 B:HIS186 3.1 28.0 1.0
OD2 B:ASP321 3.2 15.6 1.0
CE1 B:HIS325 3.4 40.0 1.0
O B:HOH2177 3.6 30.1 1.0
O B:HOH2136 3.8 39.1 1.0
CG B:HIS325 4.1 38.1 1.0
ND1 B:HIS186 4.2 28.2 1.0
CG1 B:VAL288 4.2 13.2 1.0
CG B:HIS186 4.2 27.1 1.0
CB B:ASP321 4.3 15.1 1.0
ND1 B:HIS325 4.4 40.7 1.0
CA B:ASP321 4.8 15.8 1.0
CG2 B:VAL288 4.9 12.8 1.0
O B:ASP321 4.9 19.2 1.0

Reference:

B.Herguedas, I.Lans, M.Sebastian, J.A.Hermoso, M.Martinez-Julvez, M.Medina. Structural Insights Into the Synthesis of Fmn in Prokaryotic Organisms. Acta Crystallogr.,Sect.D V. 71 2526 2015.
ISSN: ISSN 0907-4449
PubMed: 26627660
DOI: 10.1107/S1399004715019641
Page generated: Sun Oct 27 12:43:07 2024

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