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Calcium in PDB 6fhj: Structural Dynamics and Catalytic Properties of A Multi-Modular Xanthanase, Native.

Protein crystallography data

The structure of Structural Dynamics and Catalytic Properties of A Multi-Modular Xanthanase, Native., PDB code: 6fhj 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) 27.50 / 2.04
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 103.350, 103.350, 212.500, 90.00, 90.00, 120.00
R / Rfree (%) 18 / 21

Other elements in 6fhj:

The structure of Structural Dynamics and Catalytic Properties of A Multi-Modular Xanthanase, Native. also contains other interesting chemical elements:

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, Native. (pdb code 6fhj). 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, Native., PDB code: 6fhj:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 6fhj

Go back to Calcium Binding Sites List in 6fhj
Calcium binding site 1 out of 5 in the Structural Dynamics and Catalytic Properties of A Multi-Modular Xanthanase, Native.


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, Native. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca2401

b:31.2
occ:1.00
 O A:ILE197 2.2 33.6 1.0
OD1 A:ASN195 2.3 34.0 1.0
OD1 A:ASP193 2.3 34.5 1.0
OD1 A:ASP199 2.3 30.5 1.0
OD2 A:ASP202 2.4 31.8 1.0
OD1 A:ASP191 2.4 35.1 1.0
CG A:ASN195 3.3 35.0 1.0
CG A:ASP193 3.4 34.8 1.0
C A:ILE197 3.4 34.6 1.0
CG A:ASP191 3.5 36.6 1.0
CG A:ASP202 3.5 32.5 1.0
CG A:ASP199 3.6 30.5 1.0
N A:ASP199 3.8 31.3 1.0
OD2 A:ASP193 3.9 33.6 1.0
ND2 A:ASN195 3.9 34.3 1.0
CA A:ASP199 4.0 30.2 1.0
OD1 A:ASP202 4.0 33.9 1.0
CA A:ASP191 4.0 35.4 1.0
C A:PRO198 4.1 31.6 1.0
N A:ILE197 4.1 36.9 1.0
CB A:ASP191 4.2 36.5 1.0
CA A:ILE197 4.2 35.8 1.0
N A:ASN195 4.3 38.5 1.0
OD2 A:ASP191 4.4 37.7 1.0
CB A:ASP199 4.4 29.6 1.0
CB A:ILE197 4.4 35.7 1.0
CB A:ASN195 4.4 36.6 1.0
OD2 A:ASP199 4.4 30.1 1.0
N A:PRO198 4.5 33.8 1.0
O A:PRO198 4.5 31.4 1.0
C A:ASP191 4.5 35.7 1.0
NH2 A:ARG107 4.5 31.4 1.0
N A:ASP193 4.6 36.1 1.0
CA A:PRO198 4.6 33.0 1.0
CB A:ASP202 4.7 30.6 1.0
CB A:ASP193 4.7 35.3 1.0
CA A:ASN195 4.7 38.4 1.0
N A:LYS192 4.8 35.2 1.0
N A:THR194 4.8 38.7 1.0
N A:GLY196 4.9 39.5 1.0
C A:ASP193 4.9 37.7 1.0
C A:ASN195 4.9 39.1 1.0
CA A:ASP193 4.9 36.5 1.0

Calcium binding site 2 out of 5 in 6fhj

Go back to Calcium Binding Sites List in 6fhj
Calcium binding site 2 out of 5 in the Structural Dynamics and Catalytic Properties of A Multi-Modular Xanthanase, Native.


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, Native. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca2402

b:31.4
occ:1.00
 O A:GLU97 2.3 28.9 0.5
O A:GLU97 2.3 29.2 0.5
OD1 A:ASN124 2.4 36.4 1.0
O A:HOH2892 2.4 32.8 1.0
OD1 A:ASP100 2.4 28.9 1.0
O A:HOH2876 2.5 31.7 1.0
OE2 A:GLU101 2.5 27.2 1.0
OE1 A:GLU101 2.5 26.3 1.0
OD2 A:ASP100 2.8 29.2 1.0
CD A:GLU101 2.9 26.6 1.0
CG A:ASP100 3.0 29.4 1.0
C A:GLU97 3.5 28.5 0.5
C A:GLU97 3.5 28.7 0.5
CG A:ASN124 3.5 36.0 1.0
ND2 A:ASN124 4.2 37.0 1.0
N A:ASN124 4.2 33.1 1.0
CA A:TYR98 4.3 26.7 1.0
N A:TYR98 4.4 27.6 1.0
CG A:GLU101 4.4 25.6 1.0
O A:HOH2689 4.5 36.8 1.0
CB A:ASP100 4.5 29.4 1.0
CA A:GLU97 4.5 29.4 0.5
CA A:GLU97 4.5 29.7 0.5
O A:HOH3145 4.6 43.4 1.0
CB A:ASN124 4.7 35.8 1.0
N A:GLU101 4.7 26.8 1.0
OE1 A:GLU97 4.7 32.0 0.5
N A:ILE125 4.8 31.7 1.0
CD1 A:TYR98 4.8 26.3 1.0
CB A:GLU97 4.8 29.6 0.5
CA A:ASN124 4.9 34.0 1.0
CG1 A:ILE125 4.9 30.4 1.0
CD1 A:ILE125 4.9 30.3 1.0
CB A:GLU97 4.9 30.5 0.5
C A:TYR98 4.9 26.7 1.0

Calcium binding site 3 out of 5 in 6fhj

Go back to Calcium Binding Sites List in 6fhj
Calcium binding site 3 out of 5 in the Structural Dynamics and Catalytic Properties of A Multi-Modular Xanthanase, Native.


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, Native. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca2403

b:28.2
occ:1.00
 OD1 A:ASP246 2.2 29.2 1.0
O A:VAL241 2.3 30.2 1.0
OD1 A:ASN244 2.3 31.0 1.0
OD1 A:ASP247 2.3 28.2 1.0
OD1 A:ASP239 2.4 32.3 1.0
OD2 A:ASP139 2.4 27.8 1.0
CG A:ASP139 3.4 27.7 1.0
CG A:ASP246 3.4 30.1 1.0
CG A:ASN244 3.4 32.9 1.0
C A:VAL241 3.4 32.1 1.0
CG A:ASP239 3.5 33.5 1.0
CG A:ASP247 3.5 27.8 1.0
CB A:ASP139 3.7 27.9 1.0
N A:VAL241 3.7 32.6 1.0
OD2 A:ASP239 3.9 34.7 1.0
ND2 A:ASN244 3.9 33.1 1.0
OD2 A:ASP246 3.9 29.2 1.0
N A:ASP247 4.0 26.6 1.0
CA A:VAL241 4.1 33.0 1.0
OD2 A:ASP247 4.3 27.8 1.0
CB A:VAL241 4.3 34.0 1.0
CA A:ASP247 4.4 26.1 1.0
N A:ASN240 4.5 31.8 1.0
OD1 A:ASP139 4.5 26.8 1.0
C A:ASP246 4.5 27.4 1.0
N A:ASN244 4.5 32.1 1.0
N A:PRO242 4.5 32.2 1.0
CB A:ASP247 4.5 26.5 1.0
N A:ASP239 4.6 31.3 1.0
O A:HOH3086 4.6 41.2 1.0
C A:ASN240 4.7 33.3 1.0
N A:ASP246 4.7 30.6 1.0
CB A:ASP246 4.7 29.6 1.0
CB A:ASN244 4.7 33.7 1.0
CA A:PRO242 4.7 32.5 1.0
O A:ASN244 4.7 32.3 1.0
CB A:ASP239 4.8 33.5 1.0
CA A:ASP246 4.8 29.2 1.0
C A:ASN244 4.8 32.9 1.0
CB A:THR238 4.8 28.4 1.0
CA A:ASN244 4.9 32.9 1.0
C A:ASP239 4.9 32.4 1.0
C A:PRO242 4.9 32.4 1.0
N A:GLY243 4.9 31.6 1.0
CA A:ASP239 5.0 32.3 1.0
CA A:ASN240 5.0 33.0 1.0

Calcium binding site 4 out of 5 in 6fhj

Go back to Calcium Binding Sites List in 6fhj
Calcium binding site 4 out of 5 in the Structural Dynamics and Catalytic Properties of A Multi-Modular Xanthanase, Native.


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, Native. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca2404

b:21.8
occ:1.00
 OE2 A:GLU408 2.3 20.7 1.0
O A:THR404 2.4 20.8 1.0
OG A:SER642 2.4 20.3 1.0
OD1 A:ASP407 2.4 21.8 1.0
O A:HOH2600 2.5 18.8 1.0
O A:TYR641 2.5 20.6 1.0
O A:HOH2848 2.5 22.2 1.0
CG A:ASP407 3.3 22.8 1.0
CB A:SER642 3.4 20.0 1.0
C A:TYR641 3.5 20.7 1.0
CD A:GLU408 3.5 21.2 1.0
C A:THR404 3.6 20.3 1.0
OD2 A:ASP407 3.6 22.5 1.0
CA A:SER642 3.6 19.8 1.0
N A:SER642 4.0 20.2 1.0
CB A:GLU408 4.1 21.9 1.0
CG A:GLU408 4.3 20.9 1.0
N A:LEU405 4.4 20.1 1.0
CA A:THR404 4.4 20.6 1.0
OE1 A:GLU408 4.5 20.2 1.0
O A:LEU569 4.5 21.1 1.0
CA A:LEU405 4.5 20.3 1.0
CB A:THR404 4.5 20.7 1.0
N A:GLU408 4.5 22.1 1.0
O A:HOH2973 4.6 22.4 1.0
N A:LEU569 4.6 23.0 1.0
O A:HOH2932 4.7 20.0 1.0
CB A:ASP407 4.7 22.9 1.0
C A:ASP407 4.8 22.5 1.0
CA A:TYR641 4.8 21.1 1.0
CA A:GLU408 4.9 22.5 1.0
C A:LEU569 4.9 21.6 1.0
N A:TYR641 4.9 22.1 1.0
OG1 A:THR640 4.9 23.3 1.0
N A:ASP407 4.9 22.2 1.0
C A:LEU405 5.0 21.1 1.0

Calcium binding site 5 out of 5 in 6fhj

Go back to Calcium Binding Sites List in 6fhj
Calcium binding site 5 out of 5 in the Structural Dynamics and Catalytic Properties of A Multi-Modular Xanthanase, Native.


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, Native. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca2405

b:45.6
occ:1.00
 OE1 A:GLU923 2.4 40.6 1.0
OE1 A:GLU925 2.5 45.8 1.0
O A:UNK2301 2.5 49.6 1.0
OE2 A:GLU925 2.7 46.2 1.0
CD A:GLU925 2.9 46.4 1.0
CD A:GLU923 3.4 41.0 1.0
C A:UNK2301 3.7 52.2 1.0
CB A:GLU923 4.1 40.4 1.0
OE2 A:GLU923 4.2 41.6 1.0
CG A:GLU923 4.3 40.0 1.0
CA A:GLU923 4.4 40.1 1.0
N A:ALA924 4.5 43.1 1.0
CG A:GLU925 4.5 47.0 1.0
CA A:UNK2302 4.5 54.1 1.0
N A:UNK2000 4.5 40.9 1.0
N A:UNK2302 4.5 53.9 1.0
CA A:UNK2301 4.7 52.7 1.0
N A:UNK2301 4.7 52.4 1.0
C A:GLU923 4.9 41.6 1.0
CB A:UNK2000 5.0 38.3 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: Tue Jul 16 07:44:13 2024

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