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Calcium in PDB 4qaw: Structure of Modular XYN30D From Paenibacillus Barcinonensis

Enzymatic activity of Structure of Modular XYN30D From Paenibacillus Barcinonensis

All present enzymatic activity of Structure of Modular XYN30D From Paenibacillus Barcinonensis:
3.2.1.8;

Protein crystallography data

The structure of Structure of Modular XYN30D From Paenibacillus Barcinonensis, PDB code: 4qaw was solved by M.A.Sainz-Polo, J.Sanz-Aparicio, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.77 / 2.40
Space group P 32
Cell size a, b, c (Å), α, β, γ (°) 174.060, 174.060, 183.932, 90.00, 90.00, 120.00
R / Rfree (%) 19.4 / 20.2

Calcium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Calcium atom in the Structure of Modular XYN30D From Paenibacillus Barcinonensis (pdb code 4qaw). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 16 binding sites of Calcium where determined in the Structure of Modular XYN30D From Paenibacillus Barcinonensis, PDB code: 4qaw:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 16 in 4qaw

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Calcium binding site 1 out of 16 in the Structure of Modular XYN30D From Paenibacillus Barcinonensis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of Modular XYN30D From Paenibacillus Barcinonensis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1000

b:12.3
occ:1.00
 O A:GLY430 2.3 14.2 1.0
O A:THR427 2.4 15.8 1.0
O A:ASP523 2.4 10.6 1.0
OD1 A:ASP523 2.5 10.3 1.0
OE2 A:GLU409 2.5 18.3 1.0
OE1 A:GLU409 2.5 18.2 1.0
OE1 A:GLU407 2.6 20.9 1.0
CD A:GLU409 2.8 19.1 1.0
C A:ASP523 3.4 11.0 1.0
C A:THR427 3.5 16.3 1.0
C A:GLY430 3.5 14.7 1.0
CD A:GLU407 3.6 21.1 1.0
CG A:ASP523 3.7 10.4 1.0
OG1 A:THR427 3.8 17.1 1.0
CA A:ASP523 3.9 10.6 1.0
N A:THR427 4.3 15.8 1.0
N A:GLY430 4.3 15.9 1.0
CB A:GLU407 4.3 20.8 1.0
N A:GLY428 4.3 16.8 1.0
CG A:GLU409 4.4 19.4 1.0
CA A:GLY428 4.4 17.1 1.0
N A:TYR431 4.4 14.2 1.0
CA A:THR427 4.4 16.2 1.0
OE2 A:GLU407 4.4 21.2 1.0
CA A:TYR431 4.4 14.0 1.0
CB A:ASP523 4.4 10.4 1.0
CG A:GLU407 4.4 20.8 1.0
CA A:GLY430 4.5 15.2 1.0
N A:ASN524 4.5 11.5 1.0
N A:ALA408 4.5 19.3 1.0
CB A:TYR426 4.6 15.1 1.0
OD2 A:ASP523 4.6 10.6 1.0
CB A:ASN524 4.6 11.7 1.0
CA A:GLU407 4.7 20.5 1.0
CB A:THR427 4.7 16.7 1.0
C A:GLY428 4.8 17.2 1.0
CA A:ASN524 4.9 11.9 1.0
N A:SER429 4.9 17.1 1.0

Calcium binding site 2 out of 16 in 4qaw

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Calcium binding site 2 out of 16 in the Structure of Modular XYN30D From Paenibacillus Barcinonensis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of Modular XYN30D From Paenibacillus Barcinonensis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1001

b:46.3
occ:1.00
 OE1 A:GLU518 1.8 29.4 1.0
OD1 A:ASN433 2.1 15.3 1.0
O A:PHE434 2.6 21.6 1.0
CD A:GLU518 3.0 28.4 1.0
N A:PHE434 3.3 17.5 1.0
CG A:ASN433 3.3 15.1 1.0
C A:PHE434 3.6 20.2 1.0
OD1 A:ASN521 3.7 10.7 1.0
O A:GLY519 3.7 15.1 1.0
CA A:PHE434 3.8 18.9 1.0
OE2 A:GLU518 3.8 29.8 1.0
NH2 A:ARG468 3.8 20.2 1.0
CG A:GLU518 3.8 27.4 1.0
CB A:PHE434 3.9 18.6 1.0
C A:ASN433 4.0 16.3 1.0
ND2 A:ASN433 4.1 15.5 1.0
CA A:ASN433 4.2 15.3 1.0
CB A:ASN433 4.3 15.1 1.0
C A:GLY519 4.7 15.3 1.0
N A:ASN435 4.8 21.2 1.0
CG A:ASN521 4.9 10.6 1.0
CD2 A:PHE434 4.9 18.2 1.0
CG A:PHE434 5.0 18.3 1.0

Calcium binding site 3 out of 16 in 4qaw

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Calcium binding site 3 out of 16 in the Structure of Modular XYN30D From Paenibacillus Barcinonensis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of Modular XYN30D From Paenibacillus Barcinonensis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1000

b:7.6
occ:1.00
 OE1 B:GLU407 2.2 9.7 1.0
OE1 B:GLU409 2.3 14.6 1.0
OD1 B:ASP523 2.4 8.0 1.0
OE2 B:GLU409 2.4 14.7 1.0
O B:GLY430 2.5 11.2 1.0
O B:THR427 2.5 12.2 1.0
O B:ASP523 2.6 9.1 1.0
CD B:GLU409 2.7 14.5 1.0
CD B:GLU407 3.3 9.9 1.0
C B:ASP523 3.5 8.8 1.0
CG B:ASP523 3.6 8.2 1.0
C B:THR427 3.6 12.4 1.0
C B:GLY430 3.6 11.4 1.0
CA B:ASP523 3.9 8.6 1.0
OE2 B:GLU407 4.0 9.7 1.0
OG1 B:THR427 4.0 12.4 1.0
CG B:GLU409 4.2 14.5 1.0
N B:GLY430 4.3 12.0 1.0
CG B:GLU407 4.3 9.9 1.0
CB B:ASP523 4.3 8.3 1.0
N B:THR427 4.4 13.3 1.0
CB B:GLU407 4.4 10.2 1.0
CA B:TYR431 4.5 11.4 1.0
N B:TYR431 4.5 11.3 1.0
N B:GLY428 4.5 12.1 1.0
OD2 B:ASP523 4.5 7.9 1.0
CA B:GLY428 4.5 12.4 1.0
CA B:THR427 4.5 12.7 1.0
N B:ALA408 4.6 11.3 1.0
CA B:GLY430 4.6 11.6 1.0
N B:ASN524 4.6 9.2 1.0
CB B:TYR426 4.7 15.2 1.0
CB B:ASN524 4.7 9.8 1.0
CA B:GLU407 4.8 10.4 1.0
C B:GLY428 4.8 12.2 1.0
N B:SER429 4.8 12.2 1.0
CB B:THR427 4.9 12.6 1.0
CD1 B:TYR426 4.9 16.0 1.0
CB B:TYR431 4.9 11.1 1.0
CB B:GLU409 4.9 14.6 1.0
N B:GLU409 5.0 13.4 1.0

Calcium binding site 4 out of 16 in 4qaw

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Calcium binding site 4 out of 16 in the Structure of Modular XYN30D From Paenibacillus Barcinonensis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of Modular XYN30D From Paenibacillus Barcinonensis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1001

b:24.0
occ:1.00
 OE2 B:GLU518 1.3 24.3 1.0
OD1 B:ASN433 2.3 18.1 1.0
CD B:GLU518 2.5 23.7 1.0
O B:PHE434 2.5 20.1 1.0
OE1 B:GLU518 3.1 24.7 1.0
CG B:ASN433 3.4 17.3 1.0
CG B:GLU518 3.6 22.6 1.0
C B:PHE434 3.6 20.1 1.0
ND2 B:ASN433 3.8 17.2 1.0
N B:PHE434 3.9 18.1 1.0
NH2 B:ARG468 4.1 19.8 1.0
O B:GLY519 4.2 15.2 1.0
CA B:PHE434 4.2 18.8 1.0
CB B:PHE434 4.5 18.5 1.0
C B:ASN433 4.5 17.3 1.0
OD1 B:ASN521 4.6 10.6 1.0
CB B:ASN433 4.6 16.8 1.0
N B:ASN435 4.7 21.5 1.0
CA B:ASN433 4.8 16.4 1.0
CB B:GLU518 5.0 21.4 1.0
CA B:ASN435 5.0 22.9 1.0

Calcium binding site 5 out of 16 in 4qaw

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Calcium binding site 5 out of 16 in the Structure of Modular XYN30D From Paenibacillus Barcinonensis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Structure of Modular XYN30D From Paenibacillus Barcinonensis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca1000

b:6.9
occ:1.00
 OD1 C:ASP523 2.3 8.9 1.0
O C:THR427 2.4 12.8 1.0
O C:ASP523 2.4 10.2 1.0
OE1 C:GLU407 2.4 11.2 1.0
OE1 C:GLU409 2.5 14.0 1.0
O C:GLY430 2.5 11.0 1.0
OE2 C:GLU409 2.5 13.4 1.0
CD C:GLU409 2.8 14.0 1.0
C C:ASP523 3.3 10.1 1.0
CG C:ASP523 3.5 9.2 1.0
C C:THR427 3.5 13.5 1.0
OG1 C:THR427 3.5 14.2 1.0
CD C:GLU407 3.5 11.3 1.0
C C:GLY430 3.7 11.1 1.0
CA C:ASP523 3.8 9.7 1.0
N C:THR427 4.1 13.4 1.0
CB C:ASP523 4.3 9.4 1.0
CA C:THR427 4.3 13.5 1.0
OE2 C:GLU407 4.3 11.2 1.0
CB C:GLU407 4.3 11.5 1.0
CG C:GLU409 4.4 14.0 1.0
N C:ASN524 4.4 10.5 1.0
OD2 C:ASP523 4.4 9.1 1.0
CB C:ASN524 4.4 11.1 1.0
CG C:GLU407 4.4 11.3 1.0
N C:ALA408 4.5 12.0 1.0
N C:GLY430 4.5 12.7 1.0
N C:GLY428 4.5 13.6 1.0
CB C:TYR426 4.5 12.4 1.0
CB C:THR427 4.5 14.0 1.0
N C:TYR431 4.5 10.2 1.0
CA C:TYR431 4.5 9.8 1.0
CA C:GLY428 4.6 13.8 1.0
CA C:GLU407 4.6 11.8 1.0
CA C:GLY430 4.7 12.0 1.0
CA C:ASN524 4.8 10.8 1.0
ND2 C:ASN524 4.9 11.2 1.0
C C:TYR426 4.9 12.9 1.0

Calcium binding site 6 out of 16 in 4qaw

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Calcium binding site 6 out of 16 in the Structure of Modular XYN30D From Paenibacillus Barcinonensis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Structure of Modular XYN30D From Paenibacillus Barcinonensis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca1001

b:21.2
occ:1.00
 OD1 C:ASN433 2.0 11.3 1.0
O C:PHE434 2.3 16.8 1.0
OE2 C:GLU518 2.4 21.3 1.0
CG C:ASN433 3.2 11.4 1.0
C C:PHE434 3.4 16.9 1.0
N C:PHE434 3.6 14.4 1.0
CD C:GLU518 3.6 21.1 1.0
ND2 C:ASN433 3.9 11.2 1.0
CA C:PHE434 4.0 15.6 1.0
C C:ASN433 4.2 12.9 1.0
OD1 C:ASN521 4.2 12.3 1.0
NH2 C:ARG468 4.2 13.6 1.0
CG C:GLU518 4.3 20.5 1.0
CB C:PHE434 4.3 15.6 1.0
O C:GLY519 4.4 15.3 1.0
CB C:ASN433 4.4 11.6 1.0
CA C:ASN433 4.4 11.8 1.0
OE1 C:GLU518 4.5 21.9 1.0
N C:ASN435 4.6 19.0 1.0
CA C:ASN435 4.9 20.2 1.0
O C:ASN433 5.0 13.0 1.0

Calcium binding site 7 out of 16 in 4qaw

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Calcium binding site 7 out of 16 in the Structure of Modular XYN30D From Paenibacillus Barcinonensis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Structure of Modular XYN30D From Paenibacillus Barcinonensis within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca1000

b:16.6
occ:1.00
 OE1 D:GLU407 2.2 19.6 1.0
OE1 D:GLU409 2.3 21.8 1.0
OD1 D:ASP523 2.4 14.6 1.0
OE2 D:GLU409 2.4 21.9 1.0
O D:GLY430 2.5 18.8 1.0
O D:THR427 2.5 19.6 1.0
CD D:GLU409 2.7 22.6 1.0
O D:ASP523 2.7 15.4 1.0
CD D:GLU407 3.3 20.2 1.0
CG D:ASP523 3.5 14.8 1.0
C D:GLY430 3.6 18.5 1.0
C D:ASP523 3.6 15.4 1.0
C D:THR427 3.6 19.6 1.0
OG1 D:THR427 3.8 18.7 1.0
OE2 D:GLU407 3.9 20.2 1.0
CA D:ASP523 3.9 15.0 1.0
CG D:GLU409 4.2 23.3 1.0
N D:GLY430 4.2 19.9 1.0
N D:THR427 4.2 19.6 1.0
OD2 D:ASP523 4.3 15.0 1.0
CG D:GLU407 4.3 20.5 1.0
CB D:ASP523 4.3 15.0 1.0
CB D:GLU407 4.4 20.7 1.0
CA D:THR427 4.4 19.3 1.0
N D:TYR431 4.4 17.5 1.0
CA D:GLY430 4.4 19.0 1.0
N D:GLY428 4.4 19.9 1.0
N D:ALA408 4.4 21.4 1.0
CA D:TYR431 4.5 17.3 1.0
CA D:GLY428 4.5 20.7 1.0
CB D:TYR426 4.7 20.9 1.0
N D:ASN524 4.7 15.7 1.0
CB D:ASN524 4.7 16.2 1.0
CA D:GLU407 4.7 21.1 1.0
CB D:THR427 4.7 19.0 1.0
N D:SER429 4.8 21.4 1.0
C D:GLY428 4.9 21.4 1.0
N D:GLU409 4.9 24.2 1.0
CB D:GLU409 5.0 23.9 1.0

Calcium binding site 8 out of 16 in 4qaw

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Calcium binding site 8 out of 16 in the Structure of Modular XYN30D From Paenibacillus Barcinonensis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Structure of Modular XYN30D From Paenibacillus Barcinonensis within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca1001

b:44.3
occ:1.00
 OD1 D:ASN433 2.1 22.8 1.0
OE2 D:GLU518 2.2 34.6 1.0
O D:PHE434 2.4 29.3 1.0
CG D:ASN433 3.1 22.4 1.0
CD D:GLU518 3.2 33.4 1.0
ND2 D:ASN433 3.5 22.8 1.0
C D:PHE434 3.6 27.8 1.0
N D:PHE434 3.8 23.1 1.0
CG D:GLU518 3.9 31.6 1.0
NH2 D:ARG468 4.0 23.2 1.0
OE1 D:GLU518 4.1 34.6 1.0
CA D:PHE434 4.2 25.4 1.0
OD1 D:ASN521 4.2 15.0 1.0
C D:ASN433 4.3 21.6 1.0
CB D:ASN433 4.4 21.6 1.0
O D:GLY519 4.5 21.7 1.0
CB D:PHE434 4.5 24.5 1.0
CA D:ASN433 4.6 20.9 1.0
N D:ASN435 4.7 30.8 1.0
CA D:ASN435 4.9 33.1 1.0
O D:ASN433 5.0 20.7 1.0

Calcium binding site 9 out of 16 in 4qaw

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Calcium binding site 9 out of 16 in the Structure of Modular XYN30D From Paenibacillus Barcinonensis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Structure of Modular XYN30D From Paenibacillus Barcinonensis within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca1000

b:14.2
occ:1.00
 OD1 E:ASP523 2.1 11.0 1.0
O E:GLY430 2.3 13.7 1.0
OE1 E:GLU407 2.3 14.2 1.0
O E:THR427 2.4 14.3 1.0
OE2 E:GLU409 2.4 16.2 1.0
OE1 E:GLU409 2.7 16.2 1.0
O E:ASP523 2.8 11.6 1.0
CD E:GLU409 2.9 16.8 1.0
CG E:ASP523 3.3 10.8 1.0
CD E:GLU407 3.4 14.5 1.0
C E:THR427 3.4 14.6 1.0
C E:GLY430 3.5 13.4 1.0
OG1 E:THR427 3.5 14.8 1.0
C E:ASP523 3.6 11.3 1.0
CA E:ASP523 4.0 10.8 1.0
OD2 E:ASP523 4.0 10.9 1.0
N E:THR427 4.1 14.7 1.0
OE2 E:GLU407 4.1 14.2 1.0
N E:GLY430 4.2 14.4 1.0
CB E:ASP523 4.2 10.8 1.0
CA E:THR427 4.2 14.7 1.0
N E:TYR431 4.3 12.6 1.0
N E:GLY428 4.3 14.7 1.0
CG E:GLU407 4.4 14.7 1.0
CA E:GLY430 4.4 13.9 1.0
CG E:GLU409 4.4 17.5 1.0
CA E:TYR431 4.4 12.1 1.0
CB E:GLU407 4.4 14.9 1.0
CB E:TYR426 4.4 14.8 1.0
CB E:THR427 4.5 14.9 1.0
CA E:GLY428 4.5 15.0 1.0
N E:ASN524 4.6 11.8 1.0
CB E:ASN524 4.7 12.1 1.0
N E:ALA408 4.7 15.5 1.0
CB E:TYR431 4.8 11.8 1.0
N E:SER429 4.8 15.1 1.0
C E:GLY428 4.8 15.0 1.0
CA E:GLU407 4.8 15.0 1.0
C E:TYR426 4.9 14.7 1.0
CD1 E:TYR426 4.9 15.0 1.0

Calcium binding site 10 out of 16 in 4qaw

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Calcium binding site 10 out of 16 in the Structure of Modular XYN30D From Paenibacillus Barcinonensis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Structure of Modular XYN30D From Paenibacillus Barcinonensis within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca1001

b:41.6
occ:1.00
 OE2 E:GLU518 2.1 26.4 1.0
OD1 E:ASN433 2.5 16.2 1.0
CG E:ASN433 3.3 16.1 1.0
CD E:GLU518 3.3 24.5 1.0
ND2 E:ASN433 3.5 16.2 1.0
O E:PHE434 3.5 19.6 1.0
NH2 E:ARG468 3.9 14.8 1.0
OD1 E:ASN521 4.0 8.8 1.0
OE1 E:GLU518 4.0 26.8 1.0
CG E:GLU518 4.3 22.1 1.0
C E:PHE434 4.6 19.2 1.0
N E:PHE434 4.7 16.7 1.0
CB E:ASN433 4.7 15.7 1.0
O E:GLY519 4.8 11.1 1.0

Reference:

M.A.Sainz-Polo, S.V.Valenzuela, B.Gonzalez, F.I.Pastor, J.Sanz-Aparicio. Structural Analysis of Glucuronoxylan Specific XYN30D and Its Attached CBM35 Domain Give Insights Into the Role of Modularity in Specificity. J.Biol.Chem. 2014.
ISSN: ESSN 1083-351X
PubMed: 25202007
DOI: 10.1074/JBC.M114.597732
Page generated: Sun Jul 14 12:23:23 2024

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