Atomistry » Calcium » PDB 3pe0-3pty » 3pk0
Atomistry »
  Calcium »
    PDB 3pe0-3pty »
      3pk0 »

Calcium in PDB 3pk0: Crystal Structure of Short-Chain Dehydrogenase/Reductase Sdr From Mycobacterium Smegmatis

Protein crystallography data

The structure of Crystal Structure of Short-Chain Dehydrogenase/Reductase Sdr From Mycobacterium Smegmatis, PDB code: 3pk0 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) 41.23 / 1.75
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 90.140, 78.010, 155.430, 90.00, 102.22, 90.00
R / Rfree (%) 15 / 18.3

Other elements in 3pk0:

The structure of Crystal Structure of Short-Chain Dehydrogenase/Reductase Sdr From Mycobacterium Smegmatis also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Short-Chain Dehydrogenase/Reductase Sdr From Mycobacterium Smegmatis (pdb code 3pk0). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Crystal Structure of Short-Chain Dehydrogenase/Reductase Sdr From Mycobacterium Smegmatis, PDB code: 3pk0:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 3pk0

Go back to Calcium Binding Sites List in 3pk0
Calcium binding site 1 out of 8 in the Crystal Structure of Short-Chain Dehydrogenase/Reductase Sdr 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 Short-Chain Dehydrogenase/Reductase Sdr From Mycobacterium Smegmatis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca270

b:26.2
occ:0.50
 CA A:CA270 0.0 26.2 0.5
CA A:CA270 1.5 24.1 0.5
OD1 A:ASP97 2.2 18.2 1.0
O A:HOH598 2.4 33.5 1.0
O A:HOH291 2.5 10.0 1.0
CG A:ASP97 3.2 17.8 1.0
OD2 A:ASP97 3.5 18.7 1.0
N A:ASP97 4.5 13.5 1.0
CB A:ASP97 4.5 13.7 1.0
O A:HOH341 4.6 13.5 1.0

Calcium binding site 2 out of 8 in 3pk0

Go back to Calcium Binding Sites List in 3pk0
Calcium binding site 2 out of 8 in the Crystal Structure of Short-Chain Dehydrogenase/Reductase Sdr 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 Short-Chain Dehydrogenase/Reductase Sdr From Mycobacterium Smegmatis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca270

b:24.1
occ:0.50
 CA A:CA270 0.0 24.1 0.5
CA A:CA270 1.5 26.2 0.5
OD1 A:ASP97 2.4 18.2 1.0
O A:HOH598 3.2 33.5 1.0
CG A:ASP97 3.6 17.8 1.0
O A:HOH291 3.6 10.0 1.0
N A:ASP97 4.1 13.5 1.0
OD2 A:ASP97 4.2 18.7 1.0
O A:ASP97 4.4 12.8 1.0
CB A:ASP97 4.8 13.7 1.0
CA A:PRO96 4.9 15.4 1.0
CA A:ASP97 4.9 13.5 1.0
O A:HOH341 5.0 13.5 1.0

Calcium binding site 3 out of 8 in 3pk0

Go back to Calcium Binding Sites List in 3pk0
Calcium binding site 3 out of 8 in the Crystal Structure of Short-Chain Dehydrogenase/Reductase Sdr 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 Short-Chain Dehydrogenase/Reductase Sdr From Mycobacterium Smegmatis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca280

b:37.3
occ:1.00
 OD1 A:ASP51 2.3 27.7 1.0
O A:HOH319 2.3 8.9 1.0
O A:ASP51 2.3 26.2 1.0
O A:GLY54 2.4 21.6 1.0
O A:GLY56 2.4 22.9 1.0
O A:HOH283 2.4 6.4 1.0
C A:ASP51 3.3 25.8 1.0
CG A:ASP51 3.4 31.6 1.0
C A:GLY54 3.5 21.2 1.0
C A:GLY56 3.6 22.6 1.0
CA A:ASP51 3.6 25.7 1.0
N A:GLY56 4.0 20.7 1.0
C A:SER55 4.1 21.1 1.0
CB A:ASP51 4.1 26.8 1.0
CA A:GLY56 4.3 21.2 1.0
N A:GLY54 4.3 21.6 1.0
N A:SER55 4.4 21.0 1.0
OD2 A:ASP51 4.4 39.2 1.0
CA A:SER55 4.4 21.3 1.0
O A:HOH266 4.5 7.3 1.0
O A:SER55 4.5 21.4 1.0
CA A:GLY54 4.5 21.1 1.0
N A:GLN52 4.5 25.5 1.0
CG2 A:VAL58 4.5 20.6 1.0
O A:LEU50 4.6 21.0 1.0
N A:LYS57 4.6 22.6 1.0
CA A:LYS57 4.8 23.1 1.0
O A:HOH490 4.9 22.8 1.0
N A:ASP51 4.9 23.6 1.0
N A:VAL58 5.0 22.2 1.0

Calcium binding site 4 out of 8 in 3pk0

Go back to Calcium Binding Sites List in 3pk0
Calcium binding site 4 out of 8 in the Crystal Structure of Short-Chain Dehydrogenase/Reductase Sdr From Mycobacterium Smegmatis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Short-Chain Dehydrogenase/Reductase Sdr From Mycobacterium Smegmatis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca270

b:17.9
occ:0.50
 CA B:CA270 0.0 17.9 0.5
CA B:CA270 1.5 32.8 0.5
O B:HOH331 2.1 18.8 1.0
O B:HOH772 2.3 37.3 1.0
OD1 B:ASP97 2.4 18.0 1.0
CG B:ASP97 3.6 17.4 1.0
O B:HOH291 3.8 4.2 1.0
OD2 B:ASP97 4.2 17.9 1.0
N B:ASP97 4.2 12.6 1.0
O B:ASP97 4.4 13.0 1.0
CB B:ASP97 4.8 13.2 1.0
CA B:ASP97 4.9 12.1 1.0
O B:HOH277 5.0 11.2 1.0
CA B:PRO96 5.0 15.5 1.0

Calcium binding site 5 out of 8 in 3pk0

Go back to Calcium Binding Sites List in 3pk0
Calcium binding site 5 out of 8 in the Crystal Structure of Short-Chain Dehydrogenase/Reductase Sdr From Mycobacterium Smegmatis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of Short-Chain Dehydrogenase/Reductase Sdr From Mycobacterium Smegmatis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca270

b:32.8
occ:0.50
 CA B:CA270 0.0 32.8 0.5
CA B:CA270 1.5 17.9 0.5
OD1 B:ASP97 2.2 18.0 1.0
O B:HOH772 2.4 37.3 1.0
O B:HOH291 2.6 4.2 1.0
CG B:ASP97 3.1 17.4 1.0
O B:HOH331 3.2 18.8 1.0
OD2 B:ASP97 3.4 17.9 1.0
CB B:ASP97 4.5 13.2 1.0
N B:ASP97 4.6 12.6 1.0
O B:HOH277 4.7 11.2 1.0
O B:ASP97 5.0 13.0 1.0

Calcium binding site 6 out of 8 in 3pk0

Go back to Calcium Binding Sites List in 3pk0
Calcium binding site 6 out of 8 in the Crystal Structure of Short-Chain Dehydrogenase/Reductase Sdr From Mycobacterium Smegmatis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of Short-Chain Dehydrogenase/Reductase Sdr From Mycobacterium Smegmatis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca280

b:47.5
occ:1.00
 O B:GLY56 2.4 24.7 1.0
O B:ASP51 2.4 28.7 1.0
O B:GLY54 2.5 27.9 1.0
O B:HOH319 2.5 7.9 1.0
O B:HOH431 2.5 20.0 1.0
OD1 B:ASP51 2.7 34.8 1.0
C B:ASP51 3.4 28.5 1.0
C B:GLY54 3.6 26.9 1.0
CG B:ASP51 3.6 32.8 1.0
C B:GLY56 3.6 24.9 1.0
CA B:ASP51 3.7 28.1 1.0
N B:GLY56 4.0 25.6 1.0
C B:SER55 4.1 27.0 1.0
CB B:ASP51 4.2 29.4 1.0
N B:GLY54 4.3 26.4 1.0
N B:SER55 4.4 26.6 1.0
CA B:GLY56 4.4 24.4 1.0
O B:HOH281 4.4 7.7 1.0
O B:SER55 4.5 28.6 1.0
OD2 B:ASP51 4.5 37.5 1.0
CA B:SER55 4.5 27.9 1.0
CA B:GLY54 4.5 26.3 1.0
N B:LYS57 4.6 24.8 1.0
N B:GLN52 4.6 28.8 1.0
O B:LEU50 4.6 24.3 1.0
CG2 B:VAL58 4.7 23.1 1.0
CA B:LYS57 4.7 25.2 1.0
N B:VAL58 4.8 23.8 1.0
N B:ASP51 4.9 26.1 1.0

Calcium binding site 7 out of 8 in 3pk0

Go back to Calcium Binding Sites List in 3pk0
Calcium binding site 7 out of 8 in the Crystal Structure of Short-Chain Dehydrogenase/Reductase Sdr From Mycobacterium Smegmatis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of Short-Chain Dehydrogenase/Reductase Sdr From Mycobacterium Smegmatis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca280

b:50.2
occ:1.00
 O C:ASP51 2.3 32.1 1.0
O C:HOH532 2.4 25.9 1.0
O C:GLY54 2.4 29.2 1.0
O C:HOH311 2.4 11.6 1.0
O C:GLY56 2.5 27.9 1.0
OD1 C:ASP51 2.7 37.2 1.0
C C:ASP51 3.2 31.6 1.0
C C:GLY54 3.5 28.5 1.0
CA C:ASP51 3.6 31.3 1.0
CG C:ASP51 3.6 36.1 1.0
C C:GLY56 3.6 26.8 1.0
N C:GLY56 3.9 26.7 1.0
C C:SER55 4.1 28.7 1.0
CB C:ASP51 4.2 32.5 1.0
N C:SER55 4.3 28.5 1.0
N C:GLY54 4.3 28.0 1.0
CA C:SER55 4.4 29.4 1.0
CA C:GLY56 4.4 26.3 1.0
O C:HOH268 4.4 10.9 1.0
N C:GLN52 4.4 32.2 1.0
OD2 C:ASP51 4.5 39.7 1.0
CA C:GLY54 4.5 27.6 1.0
O C:LEU50 4.6 25.9 1.0
O C:SER55 4.6 28.5 1.0
N C:LYS57 4.7 26.9 1.0
CA C:LYS57 4.8 27.3 1.0
CG2 C:VAL58 4.8 26.2 1.0
N C:ASP51 4.8 29.5 1.0
CA C:GLN52 5.0 34.0 1.0

Calcium binding site 8 out of 8 in 3pk0

Go back to Calcium Binding Sites List in 3pk0
Calcium binding site 8 out of 8 in the Crystal Structure of Short-Chain Dehydrogenase/Reductase Sdr From Mycobacterium Smegmatis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of Short-Chain Dehydrogenase/Reductase Sdr From Mycobacterium Smegmatis within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca280

b:19.3
occ:1.00
 OD1 D:ASP51 2.3 22.8 1.0
O D:GLY56 2.3 20.1 1.0
O D:ASP51 2.4 20.9 1.0
O D:GLY54 2.4 20.3 1.0
O D:HOH315 2.4 4.3 1.0
C D:ASP51 3.3 20.7 1.0
CG D:ASP51 3.4 21.9 1.0
C D:GLY54 3.5 20.4 1.0
C D:GLY56 3.6 20.8 1.0
CA D:ASP51 3.7 20.4 1.0
N D:GLY56 4.1 19.8 1.0
CB D:ASP51 4.1 21.6 1.0
C D:SER55 4.2 21.1 1.0
N D:SER55 4.3 20.4 1.0
N D:GLY54 4.3 20.6 1.0
OD2 D:ASP51 4.4 25.6 1.0
CA D:SER55 4.4 21.5 1.0
CA D:GLY56 4.4 19.3 1.0
O D:HOH260 4.4 6.3 1.0
CA D:GLY54 4.5 20.0 1.0
N D:LYS57 4.5 20.8 1.0
N D:GLN52 4.6 20.6 1.0
CA D:LYS57 4.6 22.4 1.0
O D:SER55 4.7 20.5 1.0
O D:LEU50 4.8 18.8 1.0
N D:VAL58 4.8 21.8 1.0
CG2 D:VAL58 4.8 18.6 1.0
O D:HOH688 5.0 37.1 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 15:30:08 2025

Last articles

Fe in 6GAL
Fe in 6G7R
Fe in 6G72
Fe in 6G7M
Fe in 6G74
Fe in 6G7Q
Fe in 6G7P
Fe in 6G7N
Fe in 6G71
Fe in 6G2J
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy