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Calcium in PDB 3p2y: Crystal Structure of Alanine Dehydrogenase/Pyridine Nucleotide Transhydrogenase From Mycobacterium Smegmatis

Enzymatic activity of Crystal Structure of Alanine Dehydrogenase/Pyridine Nucleotide Transhydrogenase From Mycobacterium Smegmatis

All present enzymatic activity of Crystal Structure of Alanine Dehydrogenase/Pyridine Nucleotide Transhydrogenase From Mycobacterium Smegmatis:
1.4.1.1;

Protein crystallography data

The structure of Crystal Structure of Alanine Dehydrogenase/Pyridine Nucleotide Transhydrogenase From Mycobacterium Smegmatis, PDB code: 3p2y was solved by Seattle Structural Genomics Center For Infectious Disease (Ssgcid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.15 / 1.82
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 89.760, 89.760, 179.570, 90.00, 90.00, 120.00
R / Rfree (%) 16.5 / 19.6

Other elements in 3p2y:

The structure of Crystal Structure of Alanine Dehydrogenase/Pyridine Nucleotide Transhydrogenase From Mycobacterium Smegmatis also contains other interesting chemical elements:

Sodium (Na) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Alanine Dehydrogenase/Pyridine Nucleotide Transhydrogenase From Mycobacterium Smegmatis (pdb code 3p2y). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Crystal Structure of Alanine Dehydrogenase/Pyridine Nucleotide Transhydrogenase From Mycobacterium Smegmatis, PDB code: 3p2y:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 3p2y

Go back to Calcium Binding Sites List in 3p2y
Calcium binding site 1 out of 3 in the Crystal Structure of Alanine Dehydrogenase/Pyridine Nucleotide Transhydrogenase From Mycobacterium Smegmatis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Alanine Dehydrogenase/Pyridine Nucleotide Transhydrogenase From Mycobacterium Smegmatis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca361

b:22.8
occ:0.50
 O A:HOH701 2.3 33.2 0.5
O A:HOH702 2.4 23.3 1.0
O A:HOH703 2.4 23.9 1.0
O A:MET1 2.5 23.0 1.0
C A:MET1 3.5 23.9 1.0
OD2 A:ASP65 4.0 17.3 1.0
CA A:MET1 4.0 26.2 1.0
O A:HOH704 4.1 36.7 1.0
CB A:MET1 4.2 27.1 1.0
OD1 A:ASP65 4.6 18.6 1.0
N A:THR2 4.6 20.9 1.0
CG A:ASP65 4.7 16.8 1.0

Calcium binding site 2 out of 3 in 3p2y

Go back to Calcium Binding Sites List in 3p2y
Calcium binding site 2 out of 3 in the Crystal Structure of Alanine Dehydrogenase/Pyridine Nucleotide Transhydrogenase From Mycobacterium Smegmatis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Alanine Dehydrogenase/Pyridine Nucleotide Transhydrogenase From Mycobacterium Smegmatis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca362

b:26.3
occ:0.50
 O A:HOH571 2.3 35.0 1.0
O A:HOH707 2.3 39.0 1.0
O A:GLY55 2.3 16.4 1.0
O A:HOH557 2.5 27.0 1.0
C A:GLY55 3.5 16.6 1.0
CA A:GLY55 4.3 16.1 1.0
OG A:SER28 4.5 22.3 1.0
N A:ALA56 4.5 15.6 1.0
CA A:ALA56 4.5 15.2 1.0
CA A:GLU33 4.6 17.1 1.0
N A:VAL34 4.6 14.7 1.0
O A:LEU32 4.7 19.0 1.0
CG2 A:THR57 4.7 19.0 0.7
C A:ALA56 4.8 15.6 1.0
O A:VAL34 4.8 13.1 1.0
N A:THR57 4.9 15.5 1.0
OG1 A:THR57 5.0 17.2 0.3
CB A:GLU33 5.0 18.3 1.0

Calcium binding site 3 out of 3 in 3p2y

Go back to Calcium Binding Sites List in 3p2y
Calcium binding site 3 out of 3 in the Crystal Structure of Alanine Dehydrogenase/Pyridine Nucleotide Transhydrogenase From Mycobacterium Smegmatis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Alanine Dehydrogenase/Pyridine Nucleotide Transhydrogenase From Mycobacterium Smegmatis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca363

b:25.8
occ:0.50
 O A:HOH671 2.3 40.6 1.0
O A:ASP331 2.3 19.3 1.0
O A:HOH503 2.4 44.2 1.0
O A:LEU334 2.5 26.6 1.0
C A:ASP331 3.6 19.8 1.0
C A:LEU334 3.6 26.4 1.0
O A:LEU332 4.4 23.9 1.0
N A:LEU334 4.4 23.8 1.0
CA A:LEU334 4.4 25.6 1.0
CA A:ASP331 4.4 18.9 1.0
N A:LEU332 4.5 20.0 1.0
C A:LEU332 4.5 22.6 1.0
CA A:LEU332 4.5 21.8 1.0
O A:HOH736 4.6 45.1 1.0
N A:THR335 4.6 28.5 1.0
CB A:LEU334 4.6 25.3 1.0
CA A:THR335 4.7 30.3 1.0
CB A:ASP331 4.8 19.7 1.0

Reference:

L.Baugh, I.Phan, D.W.Begley, M.C.Clifton, B.Armour, D.M.Dranow, B.M.Taylor, M.M.Muruthi, J.Abendroth, J.W.Fairman, D.Fox, S.H.Dieterich, B.L.Staker, A.S.Gardberg, R.Choi, S.N.Hewitt, A.J.Napuli, J.Myers, L.K.Barrett, Y.Zhang, M.Ferrell, E.Mundt, K.Thompkins, N.Tran, S.Lyons-Abbott, A.Abramov, A.Sekar, D.Serbzhinskiy, D.Lorimer, G.W.Buchko, R.Stacy, L.J.Stewart, T.E.Edwards, W.C.Van Voorhis, P.J.Myler. Increasing the Structural Coverage of Tuberculosis Drug Targets. Tuberculosis (Edinb) V. 95 142 2015.
ISSN: ISSN 1472-9792
PubMed: 25613812
DOI: 10.1016/J.TUBE.2014.12.003
Page generated: Tue Jul 8 15:16:09 2025

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