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:
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: Tue Jul 16 07:44:29 2024
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