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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

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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: Wed Oct 28 09:36:22 2020

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