Atomistry » Calcium » PDB 3p1o-3pdd » 3p2y
Atomistry »
  Calcium »
    PDB 3p1o-3pdd »
      3p2y »

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: Sat Jul 13 16:29:38 2024

Last articles

Zn in 1MC5
Zn in 1MFM
Zn in 1MA0
Zn in 1MED
Zn in 1MEA
Zn in 1MBX
Zn in 1MA3
Zn in 1M9O
Zn in 1M9R
Zn in 1M9Q
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy