Calcium in PDB 6fhn: Structural Dynamics and Catalytic Properties of A Multi-Modular Xanthanase (Pt Derivative)

Protein crystallography data

The structure of Structural Dynamics and Catalytic Properties of A Multi-Modular Xanthanase (Pt Derivative), PDB code: 6fhn was solved by O.V.Moroz, P.F.Jensen, S.P.Mcdonald, N.Mcgregor, E.Blagova, G.Comamala, D.R.Segura, L.Anderson, S.M.Vasu, V.P.Rao, L.Giger, R.N.Monrad, A.Svendsen, J.E.Nielsen, B.Henrissat, G.J.Davies, H.Brumer, K.Rand, K.S.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 52.29 / 2.00
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 103.270, 103.270, 210.350, 90.00, 90.00, 120.00
R / Rfree (%) 17.3 / 21

Other elements in 6fhn:

The structure of Structural Dynamics and Catalytic Properties of A Multi-Modular Xanthanase (Pt Derivative) also contains other interesting chemical elements:

Platinum (Pt) 2 atoms
Chlorine (Cl) 1 atom
Sodium (Na) 3 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Structural Dynamics and Catalytic Properties of A Multi-Modular Xanthanase (Pt Derivative) (pdb code 6fhn). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Structural Dynamics and Catalytic Properties of A Multi-Modular Xanthanase (Pt Derivative), PDB code: 6fhn:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 6fhn

Go back to Calcium Binding Sites List in 6fhn
Calcium binding site 1 out of 5 in the Structural Dynamics and Catalytic Properties of A Multi-Modular Xanthanase (Pt Derivative)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structural Dynamics and Catalytic Properties of A Multi-Modular Xanthanase (Pt Derivative) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca3006

b:41.5
occ:1.00
O A:ILE197 2.1 46.7 1.0
OD1 A:ASP193 2.2 49.0 1.0
OD2 A:ASP202 2.3 44.1 1.0
OD1 A:ASN195 2.3 46.0 1.0
OD1 A:ASP191 2.4 47.4 1.0
OD1 A:ASP199 2.4 42.6 1.0
CG A:ASN195 3.3 47.5 1.0
C A:ILE197 3.3 47.1 1.0
CG A:ASP193 3.3 48.3 1.0
CG A:ASP191 3.4 49.1 1.0
CG A:ASP202 3.4 43.2 1.0
CG A:ASP199 3.6 42.6 1.0
ND2 A:ASN195 3.7 46.5 1.0
OD2 A:ASP193 3.8 47.4 1.0
N A:ASP199 3.8 42.3 1.0
OD1 A:ASP202 3.9 44.3 1.0
CA A:ASP191 4.0 47.0 1.0
CA A:ASP199 4.0 41.1 1.0
CB A:ASP191 4.1 48.6 1.0
C A:PRO198 4.1 41.9 1.0
CA A:ILE197 4.1 49.0 1.0
N A:ILE197 4.1 50.6 1.0
CB A:ILE197 4.3 48.1 1.0
N A:ASN195 4.3 52.5 1.0
OD2 A:ASP191 4.4 50.5 1.0
N A:PRO198 4.4 45.0 1.0
C A:ASP191 4.4 48.1 1.0
CB A:ASP199 4.4 40.8 1.0
O A:PRO198 4.5 41.3 1.0
NH2 A:ARG107 4.5 41.6 1.0
OD2 A:ASP199 4.5 42.8 1.0
CA A:PRO198 4.6 44.3 1.0
CB A:ASN195 4.6 50.8 1.0
N A:ASP193 4.6 50.4 1.0
CB A:ASP202 4.6 39.6 1.0
CB A:ASP193 4.7 49.0 1.0
N A:THR194 4.8 54.1 1.0
O A:ASN195 4.8 57.3 1.0
N A:LYS192 4.8 48.0 1.0
C A:ASN195 4.8 54.9 1.0
CA A:ASN195 4.8 53.1 1.0
C A:ASP193 4.9 52.8 1.0
CA A:ASP193 4.9 51.1 1.0
CG2 A:ILE197 4.9 47.0 1.0
O A:ASP191 5.0 49.1 1.0

Calcium binding site 2 out of 5 in 6fhn

Go back to Calcium Binding Sites List in 6fhn
Calcium binding site 2 out of 5 in the Structural Dynamics and Catalytic Properties of A Multi-Modular Xanthanase (Pt Derivative)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structural Dynamics and Catalytic Properties of A Multi-Modular Xanthanase (Pt Derivative) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca3007

b:46.7
occ:1.00
O A:GLU97 2.3 41.4 1.0
OD1 A:ASN124 2.3 50.5 1.0
O A:HOH3477 2.3 47.5 1.0
OD1 A:ASP100 2.5 44.4 1.0
OE1 A:GLU101 2.5 40.8 1.0
OE2 A:GLU101 2.6 41.3 1.0
O A:HOH3241 2.6 49.6 1.0
CD A:GLU101 2.9 41.1 1.0
OD2 A:ASP100 3.0 45.1 1.0
CG A:ASP100 3.1 43.6 1.0
CG A:ASN124 3.5 51.5 1.0
C A:GLU97 3.5 40.7 1.0
ND2 A:ASN124 4.1 52.9 1.0
CA A:TYR98 4.2 37.0 1.0
N A:ASN124 4.2 46.5 1.0
N A:TYR98 4.3 38.5 1.0
CG A:GLU101 4.4 39.5 1.0
CA A:GLU97 4.5 42.9 1.0
O A:HOH3703 4.5 49.4 1.0
O A:HOH3263 4.5 46.3 1.0
CB A:ASN124 4.6 50.8 1.0
CB A:ASP100 4.6 42.4 1.0
N A:ILE125 4.7 44.0 1.0
CD1 A:TYR98 4.7 36.2 1.0
N A:GLU101 4.7 38.1 1.0
CG1 A:ILE125 4.8 41.1 0.5
CA A:ASN124 4.8 47.6 1.0
CB A:GLU97 4.8 45.0 1.0
CG1 A:ILE125 4.9 42.4 0.5
C A:TYR98 4.9 36.2 1.0
CD1 A:ILE125 5.0 39.2 0.5

Calcium binding site 3 out of 5 in 6fhn

Go back to Calcium Binding Sites List in 6fhn
Calcium binding site 3 out of 5 in the Structural Dynamics and Catalytic Properties of A Multi-Modular Xanthanase (Pt Derivative)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structural Dynamics and Catalytic Properties of A Multi-Modular Xanthanase (Pt Derivative) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca3008

b:34.0
occ:1.00
OD1 A:ASP246 2.3 37.9 1.0
OD1 A:ASP247 2.3 33.2 1.0
O A:VAL241 2.3 37.0 1.0
OD1 A:ASN244 2.3 37.4 1.0
OD1 A:ASP239 2.3 37.0 1.0
OD2 A:ASP139 2.4 34.3 1.0
CG A:ASP239 3.3 38.5 1.0
CG A:ASP139 3.4 33.1 1.0
CG A:ASN244 3.4 39.6 1.0
C A:VAL241 3.4 38.5 1.0
CG A:ASP246 3.4 38.8 1.0
CG A:ASP247 3.5 33.6 1.0
OD2 A:ASP239 3.7 39.7 1.0
CB A:ASP139 3.7 33.5 1.0
N A:VAL241 3.8 38.0 1.0
ND2 A:ASN244 3.9 40.1 1.0
OD2 A:ASP246 3.9 38.3 1.0
N A:ASP247 3.9 33.6 1.0
CA A:VAL241 4.1 39.2 1.0
OD2 A:ASP247 4.3 32.5 1.0
CB A:VAL241 4.3 40.8 1.0
CA A:ASP247 4.3 32.4 1.0
N A:ASN240 4.4 37.2 1.0
N A:ASN244 4.5 38.9 1.0
N A:PRO242 4.5 38.2 1.0
OD1 A:ASP139 4.5 32.2 1.0
N A:ASP239 4.5 36.4 1.0
C A:ASP246 4.5 34.9 1.0
CB A:ASP247 4.5 32.2 1.0
O A:HOH3709 4.6 43.1 1.0
C A:ASN240 4.6 38.0 1.0
CB A:ASN244 4.7 40.6 1.0
CB A:ASP239 4.7 39.4 1.0
N A:ASP246 4.7 38.6 1.0
CB A:ASP246 4.7 38.2 1.0
CA A:PRO242 4.7 38.0 1.0
O A:ASN244 4.7 36.2 1.0
CB A:THR238 4.8 33.5 1.0
C A:ASN244 4.8 38.7 1.0
CA A:ASP246 4.8 37.2 1.0
CA A:ASN244 4.8 39.2 1.0
C A:ASP239 4.8 38.1 1.0
CA A:ASP239 4.9 38.2 1.0
C A:PRO242 4.9 38.1 1.0
N A:GLY243 4.9 37.3 1.0
CA A:ASN240 5.0 38.0 1.0

Calcium binding site 4 out of 5 in 6fhn

Go back to Calcium Binding Sites List in 6fhn
Calcium binding site 4 out of 5 in the Structural Dynamics and Catalytic Properties of A Multi-Modular Xanthanase (Pt Derivative)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structural Dynamics and Catalytic Properties of A Multi-Modular Xanthanase (Pt Derivative) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca3009

b:26.1
occ:1.00
OE2 A:GLU408 2.3 25.6 1.0
O A:THR404 2.4 24.7 1.0
OG A:SER642 2.4 24.1 1.0
OD1 A:ASP407 2.4 25.7 1.0
O A:HOH3218 2.4 23.5 1.0
O A:TYR641 2.5 23.7 1.0
O A:HOH3440 2.6 25.8 1.0
CG A:ASP407 3.3 26.9 1.0
CB A:SER642 3.5 23.9 1.0
C A:TYR641 3.5 23.4 1.0
C A:THR404 3.5 24.8 1.0
CD A:GLU408 3.6 24.8 1.0
OD2 A:ASP407 3.6 25.8 1.0
CA A:SER642 3.6 24.1 1.0
N A:SER642 4.0 22.7 1.0
CB A:GLU408 4.1 25.7 1.0
CG A:GLU408 4.3 25.1 1.0
CA A:THR404 4.4 24.9 1.0
N A:LEU405 4.4 23.8 1.0
CB A:THR404 4.4 24.7 1.0
CA A:LEU405 4.5 24.5 1.0
OE1 A:GLU408 4.5 24.0 1.0
O A:LEU569 4.5 25.0 1.0
O A:HOH3591 4.6 27.8 1.0
N A:GLU408 4.6 26.2 1.0
N A:LEU569 4.6 26.3 1.0
CB A:ASP407 4.7 26.9 1.0
O A:HOH3635 4.7 26.6 1.0
C A:ASP407 4.8 26.8 1.0
CA A:TYR641 4.8 23.6 1.0
C A:LEU569 4.8 25.6 1.0
OG1 A:THR640 4.8 27.0 1.0
N A:TYR641 4.9 24.6 1.0
CA A:GLU408 4.9 26.8 1.0
N A:ASP407 4.9 26.3 1.0
CA A:ASP407 5.0 26.8 1.0
C A:LEU405 5.0 25.0 1.0
CD2 A:LEU405 5.0 24.9 1.0

Calcium binding site 5 out of 5 in 6fhn

Go back to Calcium Binding Sites List in 6fhn
Calcium binding site 5 out of 5 in the Structural Dynamics and Catalytic Properties of A Multi-Modular Xanthanase (Pt Derivative)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Structural Dynamics and Catalytic Properties of A Multi-Modular Xanthanase (Pt Derivative) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca3010

b:55.8
occ:1.00
OE2 A:GLU925 2.6 55.4 1.0
O A:UNK2301 2.8 62.4 1.0
OE1 A:GLU923 3.0 57.0 1.0
OE1 A:GLU925 3.2 55.4 1.0
CD A:GLU925 3.3 56.1 1.0
CD A:GLU923 3.6 56.2 1.0
N A:UNK2301 3.7 62.1 1.0
C A:UNK2301 3.9 63.4 1.0
OE2 A:GLU923 3.9 57.2 1.0
CA A:UNK2301 4.3 63.6 1.0
CG A:GLU923 4.6 53.5 1.0
CG A:GLU925 4.8 56.1 1.0
CB A:GLU923 4.8 53.5 1.0
CB A:UNK2301 4.9 62.2 1.0
N A:UNK2302 5.0 64.4 1.0

Reference:

O.V.Moroz, P.F.Jensen, S.P.Mcdonald, N.Mcgregor, E.Blagova, G.Comamala, D.R.Segura, L.Anderson, S.M.Vasu, V.P.Rao, L.Giger, R.N.Monrad, A.Svendsen, J.E.Nielsen, B.Henrissat, G.J.Davies, H.Brumer, K.Rand, K.S.Wilson. Structural Dynamics and Catalytic Properties of A Multimodular Xanthanase Acs Catalysis 2018.
ISSN: ESSN 2155-5435
DOI: 10.1021/ACSCATAL.8B00666
Page generated: Sat Dec 12 06:06:50 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy