Atomistry » Calcium » PDB 6ulw-6v4p » 6ulw
Atomistry »
  Calcium »
    PDB 6ulw-6v4p »
      6ulw »

Calcium in PDB 6ulw: Adenylation, Ketoreductase, and Pseudo Asub Multidomain Structure of A Keto Acid-Selecting Nrps Module

Protein crystallography data

The structure of Adenylation, Ketoreductase, and Pseudo Asub Multidomain Structure of A Keto Acid-Selecting Nrps Module, PDB code: 6ulw was solved by D.A.Alonzo, J.Wang, C.Chiche-Lapierre, T.M.Schmeing, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.11 / 3.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 141.660, 143.660, 431.870, 90.00, 90.00, 90.00
R / Rfree (%) 22.8 / 27.5

Other elements in 6ulw:

The structure of Adenylation, Ketoreductase, and Pseudo Asub Multidomain Structure of A Keto Acid-Selecting Nrps Module also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Adenylation, Ketoreductase, and Pseudo Asub Multidomain Structure of A Keto Acid-Selecting Nrps Module (pdb code 6ulw). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Adenylation, Ketoreductase, and Pseudo Asub Multidomain Structure of A Keto Acid-Selecting Nrps Module, PDB code: 6ulw:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 6ulw

Go back to Calcium Binding Sites List in 6ulw
Calcium binding site 1 out of 8 in the Adenylation, Ketoreductase, and Pseudo Asub Multidomain Structure of A Keto Acid-Selecting Nrps Module


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Adenylation, Ketoreductase, and Pseudo Asub Multidomain Structure of A Keto Acid-Selecting Nrps Module within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1401

b:0.1
occ:1.00
 OD2 A:ASP704 3.6 1.0 1.0
OE1 A:GLU720 3.7 0.7 1.0
OD1 A:ASP704 4.2 0.4 1.0
CG A:ASP704 4.4 0.6 1.0
CD A:GLU720 4.8 0.0 1.0

Calcium binding site 2 out of 8 in 6ulw

Go back to Calcium Binding Sites List in 6ulw
Calcium binding site 2 out of 8 in the Adenylation, Ketoreductase, and Pseudo Asub Multidomain Structure of A Keto Acid-Selecting Nrps Module


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Adenylation, Ketoreductase, and Pseudo Asub Multidomain Structure of A Keto Acid-Selecting Nrps Module within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1402

b:0.1
occ:1.00
 O A:GLU560 2.4 0.7 1.0
HA A:GLU561 3.5 0.3 1.0
C A:GLU560 3.6 0.6 1.0
O A:GLU561 3.8 0.7 1.0
C A:GLU561 4.1 0.1 1.0
CA A:GLU561 4.1 1.0 1.0
O A:VAL562 4.3 0.9 1.0
N A:GLU561 4.4 0.9 1.0
HB3 A:GLU560 4.4 0.3 1.0
O A:VAL565 4.6 0.3 1.0
HG1 A:THR567 4.6 0.8 1.0
OG1 A:THR567 4.6 1.0 1.0
HA A:PRO563 4.7 0.3 1.0
HA A:GLU560 4.7 0.6 1.0
CA A:GLU560 4.7 0.0 1.0
N A:VAL562 4.9 0.9 1.0
OE2 A:GLU1204 4.9 0.5 1.0
C A:VAL562 4.9 0.4 1.0

Calcium binding site 3 out of 8 in 6ulw

Go back to Calcium Binding Sites List in 6ulw
Calcium binding site 3 out of 8 in the Adenylation, Ketoreductase, and Pseudo Asub Multidomain Structure of A Keto Acid-Selecting Nrps Module


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Adenylation, Ketoreductase, and Pseudo Asub Multidomain Structure of A Keto Acid-Selecting Nrps Module within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1401

b:0.8
occ:1.00
 HG1 B:THR115 3.4 0.7 1.0
HD1 B:TYR345 3.4 0.7 1.0
OE2 B:GLU322 4.2 0.1 1.0
OG1 B:THR115 4.2 0.0 1.0
HB3 B:GLU322 4.3 0.8 1.0
CD1 B:TYR345 4.3 0.6 1.0
CD B:GLU322 4.4 0.6 1.0
HE1 B:TYR345 4.5 0.8 1.0
HG21 B:THR115 4.5 0.3 1.0
HG3 B:GLU322 4.5 0.7 1.0
HG11 B:VAL296 4.6 0.9 1.0
OE1 B:GLU322 4.7 1.0 1.0
HG13 B:VAL296 4.7 0.9 1.0
CE1 B:TYR345 4.8 0.3 1.0
HB3 B:TYR345 4.8 0.9 1.0
CG B:GLU322 4.9 0.0 1.0

Calcium binding site 4 out of 8 in 6ulw

Go back to Calcium Binding Sites List in 6ulw
Calcium binding site 4 out of 8 in the Adenylation, Ketoreductase, and Pseudo Asub Multidomain Structure of A Keto Acid-Selecting Nrps Module


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Adenylation, Ketoreductase, and Pseudo Asub Multidomain Structure of A Keto Acid-Selecting Nrps Module within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1402

b:0.1
occ:1.00
 O B:GLU560 2.9 0.0 1.0
HZ1 B:LYS592 3.0 0.8 1.0
O B:VAL565 3.8 0.3 1.0
NZ B:LYS592 3.8 1.0 1.0
OG1 B:THR567 3.9 0.9 1.0
HZ3 B:LYS592 4.0 0.8 1.0
HZ2 B:LYS592 4.1 0.8 1.0
HG1 B:THR567 4.1 0.7 1.0
C B:GLU560 4.1 0.2 1.0
HA B:GLU561 4.2 0.6 1.0
O B:GLU561 4.4 0.2 1.0
O B:VAL562 4.4 0.2 1.0
C B:GLU561 4.6 1.0 1.0
HA B:PRO563 4.7 0.4 1.0
HB3 B:GLU560 4.7 0.5 1.0
OE2 B:GLU1204 4.7 0.7 1.0
OD2 B:ASP362 4.7 0.2 1.0
CA B:GLU561 4.8 0.7 1.0
CE B:LYS592 4.9 0.4 1.0
HG23 B:THR567 4.9 0.1 1.0
HE2 B:LYS592 4.9 0.1 1.0
HB B:VAL565 4.9 0.3 1.0
HA B:GLU560 4.9 0.8 1.0
OD1 B:ASP362 4.9 0.0 1.0
N B:GLU561 4.9 0.8 1.0
HE3 B:LYS592 5.0 0.1 1.0
C B:VAL565 5.0 0.3 1.0

Calcium binding site 5 out of 8 in 6ulw

Go back to Calcium Binding Sites List in 6ulw
Calcium binding site 5 out of 8 in the Adenylation, Ketoreductase, and Pseudo Asub Multidomain Structure of A Keto Acid-Selecting Nrps Module


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Adenylation, Ketoreductase, and Pseudo Asub Multidomain Structure of A Keto Acid-Selecting Nrps Module within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca1401

b:0.2
occ:1.00
 OE2 C:GLU61 2.8 0.2 1.0
OD1 A:ASP652 3.6 0.1 1.0
OD2 A:ASP652 3.8 0.2 1.0
CD C:GLU61 3.8 0.1 1.0
HA A:GLN647 4.0 0.8 1.0
O A:GLN647 4.0 0.1 1.0
CG A:ASP652 4.1 0.6 1.0
HG2 C:GLU61 4.4 0.2 1.0
OE1 C:GLU61 4.5 0.9 1.0
O A:TRP646 4.5 0.9 1.0
CG C:GLU61 4.7 0.3 1.0
C A:GLN647 4.7 0.5 1.0
HA2 A:GLY649 4.8 0.5 1.0
CA A:GLN647 4.8 0.0 1.0
HA3 A:GLY649 4.9 0.5 1.0

Calcium binding site 6 out of 8 in 6ulw

Go back to Calcium Binding Sites List in 6ulw
Calcium binding site 6 out of 8 in the Adenylation, Ketoreductase, and Pseudo Asub Multidomain Structure of A Keto Acid-Selecting Nrps Module


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Adenylation, Ketoreductase, and Pseudo Asub Multidomain Structure of A Keto Acid-Selecting Nrps Module within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca1402

b:0.8
occ:1.00
 O C:GLU560 3.2 0.9 1.0
HZ1 C:LYS592 3.6 0.8 1.0
O C:VAL565 3.8 0.7 1.0
OG1 C:THR567 3.8 0.3 1.0
HG1 C:THR567 3.9 0.9 1.0
HE3 C:LYS592 4.2 0.2 1.0
HZ2 C:LYS592 4.3 0.8 1.0
NZ C:LYS592 4.3 0.6 1.0
C C:GLU560 4.5 0.1 1.0
HB3 C:GLU560 4.6 0.3 1.0
OD2 C:ASP362 4.7 0.6 1.0
CE C:LYS592 4.7 1.0 1.0
HA C:GLU561 4.8 0.4 1.0
HG23 C:THR567 4.8 0.8 1.0
OE2 C:GLU1204 4.9 0.0 1.0
O C:VAL562 4.9 0.6 1.0
HA C:PRO563 4.9 0.3 1.0
CG C:ASP362 4.9 0.9 1.0
HE2 C:LYS592 5.0 0.2 1.0

Calcium binding site 7 out of 8 in 6ulw

Go back to Calcium Binding Sites List in 6ulw
Calcium binding site 7 out of 8 in the Adenylation, Ketoreductase, and Pseudo Asub Multidomain Structure of A Keto Acid-Selecting Nrps Module


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Adenylation, Ketoreductase, and Pseudo Asub Multidomain Structure of A Keto Acid-Selecting Nrps Module within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca1402

b:0.5
occ:1.00
 OE1 D:GLU906 2.2 0.8 1.0
OD1 D:ASP998 2.3 0.3 1.0
OD2 D:ASP998 2.5 0.8 1.0
CG D:ASP998 2.7 0.5 1.0
CD D:GLU906 3.1 0.4 1.0
OE2 D:GLU906 3.5 0.4 1.0
HG3 D:ARG995 3.8 0.8 1.0
HA2 D:GLY909 3.9 0.5 1.0
O D:ARG996 4.1 0.1 1.0
CB D:ASP998 4.2 0.3 1.0
CG D:GLU906 4.4 0.5 1.0
H D:LEU910 4.5 0.9 1.0
HB2 D:GLU906 4.5 0.2 1.0
HA3 D:GLY909 4.6 0.5 1.0
HB2 D:ASP998 4.6 0.1 1.0
H D:ARG996 4.6 0.8 1.0
HB3 D:GLU906 4.6 0.2 1.0
HB3 D:ASP998 4.6 0.1 1.0
CG D:ARG995 4.6 0.0 1.0
CA D:GLY909 4.7 0.6 1.0
HG2 D:ARG995 4.7 0.8 1.0
HG3 D:GLU906 4.7 0.4 1.0
CB D:GLU906 4.8 0.5 1.0
HA D:ASP998 4.9 0.3 1.0
HB2 D:ARG996 5.0 0.8 1.0

Calcium binding site 8 out of 8 in 6ulw

Go back to Calcium Binding Sites List in 6ulw
Calcium binding site 8 out of 8 in the Adenylation, Ketoreductase, and Pseudo Asub Multidomain Structure of A Keto Acid-Selecting Nrps Module


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Adenylation, Ketoreductase, and Pseudo Asub Multidomain Structure of A Keto Acid-Selecting Nrps Module within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca1403

b:0.1
occ:1.00
 O D:GLU560 2.8 0.4 1.0
HA D:GLU561 3.7 0.8 1.0
HZ1 D:LYS592 3.9 0.7 1.0
C D:GLU560 4.0 0.3 1.0
O D:GLU561 4.1 0.0 1.0
OG1 D:THR567 4.4 0.1 1.0
CA D:GLU561 4.4 0.6 1.0
C D:GLU561 4.4 0.5 1.0
O D:VAL565 4.5 0.2 1.0
HB3 D:GLU560 4.5 0.9 1.0
HG1 D:THR567 4.7 0.3 1.0
N D:GLU561 4.7 0.7 1.0
O D:VAL562 4.7 0.1 1.0
NZ D:LYS592 4.8 0.7 1.0
OD2 D:ASP362 4.9 0.8 1.0
OD1 D:ASP362 5.0 0.9 1.0

Reference:

D.A.Alonzo, C.Chiche-Lapierre, J.Wang, M.J.Tarry, T.M.Schmeing. Structural Basis of Keto Acid Utilization in Nonribosomal Depsipeptide Synthesis Nat.Chem.Biol. 2020.
ISSN: ESSN 1552-4469
DOI: 10.1038/S41589-020-0481-5
Page generated: Wed Jul 9 18:37:15 2025

Last articles

Cl in 5RAE
Cl in 5RAD
Cl in 5RAC
Cl in 5RAB
Cl in 5RA9
Cl in 5RAA
Cl in 5RA8
Cl in 5RA7
Cl in 5RA4
Cl in 5RA6
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy