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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

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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: Tue Jul 16 16:01:06 2024

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