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Calcium in PDB 6f2p: Structure of Paenibacillus Xanthan Lyase to 2.6 A Resolution

Enzymatic activity of Structure of Paenibacillus Xanthan Lyase to 2.6 A Resolution

All present enzymatic activity of Structure of Paenibacillus Xanthan Lyase to 2.6 A Resolution:
4.2.2.12;

Protein crystallography data

The structure of Structure of Paenibacillus Xanthan Lyase to 2.6 A Resolution, PDB code: 6f2p was solved by L.Lo Leggio, A.Kadziola, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.05 / 2.60
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 100.610, 100.610, 324.830, 90.00, 90.00, 90.00
R / Rfree (%) 16.5 / 21.3

Other elements in 6f2p:

The structure of Structure of Paenibacillus Xanthan Lyase to 2.6 A Resolution also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Structure of Paenibacillus Xanthan Lyase to 2.6 A Resolution (pdb code 6f2p). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 9 binding sites of Calcium where determined in the Structure of Paenibacillus Xanthan Lyase to 2.6 A Resolution, PDB code: 6f2p:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Calcium binding site 1 out of 9 in 6f2p

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Calcium binding site 1 out of 9 in the Structure of Paenibacillus Xanthan Lyase to 2.6 A Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of Paenibacillus Xanthan Lyase to 2.6 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1101

b:20.1
occ:1.00
 OE1 A:GLU651 2.2 23.7 1.0
OE1 A:GLN636 2.3 27.4 1.0
OD1 A:ASP491 2.4 21.6 1.0
OD1 A:ASP490 2.5 21.0 1.0
OE2 A:GLU492 2.5 20.8 1.0
OE1 A:GLU492 2.5 21.2 1.0
CD A:GLU492 2.9 21.6 1.0
CG A:ASP490 3.3 17.2 1.0
CD A:GLU651 3.4 26.0 1.0
OD2 A:ASP490 3.4 22.9 1.0
CG A:ASP491 3.4 22.8 1.0
CD A:GLN636 3.5 23.0 1.0
OD2 A:ASP491 3.9 26.2 1.0
CG A:GLU651 4.0 21.9 1.0
CB A:GLN636 4.1 22.6 1.0
N A:ASP491 4.3 17.4 1.0
CG A:GLU492 4.4 12.8 1.0
NE2 A:GLN636 4.4 39.2 1.0
OE2 A:GLU651 4.4 21.6 1.0
CG A:GLN636 4.4 20.1 1.0
CB A:ASP490 4.7 18.6 1.0
CB A:ASP491 4.7 15.1 1.0
N A:ASP490 4.8 15.7 1.0
CA A:ASP491 4.9 15.8 1.0
CE2 A:TYR631 4.9 17.6 1.0
N A:GLU492 4.9 15.1 1.0
OH A:TYR631 4.9 17.9 1.0
C A:ASP491 5.0 15.2 1.0

Calcium binding site 2 out of 9 in 6f2p

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Calcium binding site 2 out of 9 in the Structure of Paenibacillus Xanthan Lyase to 2.6 A Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of Paenibacillus Xanthan Lyase to 2.6 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1102

b:24.3
occ:1.00
 OE2 A:GLU771 2.3 24.6 1.0
OD1 A:ASP894 2.3 28.7 1.0
O A:SER791 2.3 29.1 1.0
O A:LYS794 2.4 34.7 1.0
OE2 A:GLU769 2.5 26.5 1.0
OE1 A:GLU771 2.6 21.6 1.0
CD A:GLU771 2.8 27.5 1.0
O A:ASP894 2.8 28.1 1.0
C A:SER791 3.4 30.5 1.0
CG A:ASP894 3.5 31.8 1.0
CD A:GLU769 3.5 26.0 1.0
C A:LYS794 3.6 26.0 1.0
C A:ASP894 3.7 28.1 1.0
CA A:ASP894 4.1 26.1 1.0
CB A:SER791 4.1 22.9 1.0
CB A:GLU769 4.2 27.4 1.0
CA A:SER791 4.2 21.7 1.0
OE1 A:GLU769 4.2 31.8 1.0
CG A:GLU771 4.3 25.0 1.0
N A:LYS794 4.4 27.9 1.0
OD2 A:ASP894 4.4 21.6 1.0
N A:SER791 4.4 25.8 1.0
CG A:GLU769 4.4 21.1 1.0
CB A:ASP894 4.4 25.3 1.0
CA A:LYS794 4.4 26.6 1.0
N A:GLY792 4.4 26.8 1.0
CA A:GLU769 4.5 24.4 1.0
N A:LYS795 4.5 25.4 1.0
N A:ALA770 4.6 27.1 1.0
CA A:LYS795 4.6 29.2 1.0
CA A:GLY792 4.6 24.0 1.0
CB A:LYS794 4.7 29.0 1.0
N A:ASN895 4.8 27.2 1.0
CB A:ASN895 4.8 22.9 1.0
OG A:SER791 4.9 28.9 1.0
CB A:ALA790 4.9 26.5 1.0
N A:GLU771 4.9 22.6 1.0
C A:GLU769 4.9 28.8 1.0
CB A:GLU771 4.9 28.3 1.0
C A:ALA790 5.0 28.5 1.0
C A:GLY792 5.0 30.3 1.0

Calcium binding site 3 out of 9 in 6f2p

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Calcium binding site 3 out of 9 in the Structure of Paenibacillus Xanthan Lyase to 2.6 A Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of Paenibacillus Xanthan Lyase to 2.6 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1103

b:41.7
occ:1.00
 OD1 A:ASP780 2.5 36.3 1.0
OD1 A:ASN801 2.6 55.7 1.0
OD2 A:ASP805 2.6 40.5 1.0
OD1 A:ASP805 2.9 33.2 1.0
CG A:ASP805 3.1 38.7 1.0
OD2 A:ASP780 3.2 37.6 1.0
CG A:ASP780 3.2 41.5 1.0
CG A:ASN801 3.3 41.8 1.0
CB A:ASN801 3.3 35.6 1.0
N A:ASN801 4.0 41.3 1.0
CA A:ASN801 4.2 37.0 1.0
OG1 A:THR779 4.5 24.9 1.0
O A:THR779 4.5 38.5 1.0
ND2 A:ASN801 4.6 40.4 1.0
CB A:ASP805 4.6 32.4 1.0
N A:ALA802 4.6 35.4 1.0
CB A:ASP780 4.6 30.8 1.0
CB A:THR779 4.8 27.0 1.0
C A:ASN801 4.9 35.3 1.0
C A:THR779 4.9 31.3 1.0

Calcium binding site 4 out of 9 in 6f2p

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Calcium binding site 4 out of 9 in the Structure of Paenibacillus Xanthan Lyase to 2.6 A Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of Paenibacillus Xanthan Lyase to 2.6 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1104

b:28.6
occ:1.00
 OG1 A:THR333 2.3 26.1 1.0
OD1 A:ASP331 2.3 33.1 1.0
O A:HOH1636 2.4 24.2 1.0
O A:HOH1558 2.4 32.7 1.0
OD1 A:ASP329 2.4 30.3 1.0
O A:HOH1552 2.8 25.8 1.0
CG A:ASP331 3.2 29.4 1.0
OD2 A:ASP331 3.4 28.0 1.0
CB A:THR333 3.4 25.2 1.0
CG A:ASP329 3.6 27.4 1.0
O A:HOH1500 4.2 24.7 1.0
N A:THR333 4.2 23.1 1.0
OD2 A:ASP329 4.3 22.9 1.0
CG2 A:THR333 4.4 21.3 1.0
CA A:THR333 4.4 27.5 1.0
CA A:ASP329 4.5 26.8 1.0
OD2 A:ASP293 4.5 21.0 1.0
CB A:ASP329 4.6 26.0 1.0
CB A:ASP331 4.6 23.1 1.0
N A:ASP331 4.8 28.4 1.0
O A:HOH1228 4.9 16.7 1.0
C A:ASP329 4.9 31.2 1.0
CB A:ASP293 5.0 22.9 1.0

Calcium binding site 5 out of 9 in 6f2p

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Calcium binding site 5 out of 9 in the Structure of Paenibacillus Xanthan Lyase to 2.6 A Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Structure of Paenibacillus Xanthan Lyase to 2.6 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1105

b:16.7
occ:1.00
 OE1 A:GLN161 2.2 18.2 1.0
O A:HOH1569 2.3 14.6 1.0
O A:SER163 2.4 22.9 1.0
O A:HOH1224 2.5 12.1 1.0
O A:HOH1412 2.5 13.7 1.0
OE2 A:GLU174 2.5 25.5 1.0
O A:HOH1303 2.6 16.8 1.0
CD A:GLN161 3.3 15.4 1.0
CD A:GLU174 3.5 20.5 1.0
C A:SER163 3.6 20.2 1.0
CG A:GLU174 3.7 12.8 1.0
NE2 A:GLN161 3.8 14.5 1.0
N A:SER163 4.1 20.8 1.0
NE2 A:GLN127 4.1 18.8 1.0
CA A:SER163 4.4 20.1 1.0
N A:THR165 4.5 19.6 1.0
N A:VAL164 4.5 19.9 1.0
N A:ALA162 4.6 19.8 1.0
OG1 A:THR165 4.6 18.1 1.0
CG A:GLN161 4.6 13.1 1.0
OE1 A:GLU174 4.6 23.8 1.0
CA A:VAL164 4.6 15.5 1.0
OG A:SER163 4.6 20.0 1.0
CB A:GLU174 4.7 16.8 1.0
CA A:GLN161 4.8 15.6 1.0
CG2 A:THR165 4.8 15.6 1.0
C A:GLN161 4.9 18.7 1.0
C A:VAL164 4.9 18.9 1.0

Calcium binding site 6 out of 9 in 6f2p

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Calcium binding site 6 out of 9 in the Structure of Paenibacillus Xanthan Lyase to 2.6 A Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Structure of Paenibacillus Xanthan Lyase to 2.6 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1106

b:58.4
occ:1.00
 OD1 A:ASN911 2.3 57.0 1.0
O A:TYR933 2.3 58.6 1.0
O A:ASP936 2.4 72.5 1.0
OD1 A:ASP1032 2.5 56.0 1.0
OD1 A:ASP910 2.6 66.0 1.0
OD2 A:ASP910 2.9 64.3 1.0
CG A:ASP910 3.0 62.8 1.0
CG A:ASN911 3.5 62.9 1.0
C A:TYR933 3.5 61.3 1.0
C A:ASP936 3.5 72.7 1.0
CG A:ASP1032 3.8 52.1 1.0
OD1 A:ASP936 3.9 68.0 1.0
O A:ASP1032 4.0 54.9 1.0
ND2 A:ASN911 4.1 68.0 1.0
CA A:GLY934 4.2 56.1 1.0
N A:GLY934 4.2 58.7 1.0
CA A:TYR937 4.3 62.7 1.0
N A:ASN911 4.3 57.7 1.0
N A:TYR937 4.3 72.3 1.0
C A:ASP1032 4.4 54.5 1.0
CA A:ASP1032 4.4 47.8 1.0
N A:ASP936 4.5 65.4 1.0
CB A:ASP910 4.5 59.5 1.0
O A:ARG932 4.5 64.2 0.6
O A:ARG932 4.5 64.2 0.4
OD2 A:ASP1032 4.6 52.5 1.0
CA A:TYR933 4.6 64.4 1.0
CA A:ASP936 4.6 67.9 1.0
CB A:ASN911 4.6 56.7 1.0
CB A:ASP1032 4.7 45.7 1.0
C A:GLY934 4.7 56.9 1.0
CB A:TYR933 4.7 57.5 1.0
CB A:TYR937 4.7 63.4 1.0
CG A:ASP936 4.9 58.7 1.0
CA A:ASP910 5.0 53.2 1.0

Calcium binding site 7 out of 9 in 6f2p

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Calcium binding site 7 out of 9 in the Structure of Paenibacillus Xanthan Lyase to 2.6 A Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Structure of Paenibacillus Xanthan Lyase to 2.6 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1107

b:67.3
occ:1.00
 O A:GLY946 2.6 44.6 1.0
O A:HOH1665 2.7 47.8 1.0
O A:HOH1595 2.7 42.1 1.0
OD2 A:ASP1023 2.9 56.3 1.0
C A:GLY946 3.7 48.5 1.0
CG A:ASP1023 4.0 55.9 1.0
CA A:GLY946 4.1 45.7 1.0
OD1 A:ASP1023 4.4 57.3 1.0
N A:THR947 4.9 50.0 1.0

Calcium binding site 8 out of 9 in 6f2p

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Calcium binding site 8 out of 9 in the Structure of Paenibacillus Xanthan Lyase to 2.6 A Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Structure of Paenibacillus Xanthan Lyase to 2.6 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1108

b:39.6
occ:1.00
 O A:HOH1535 2.4 30.6 1.0
O A:GLY565 2.5 19.1 1.0
C A:GLY565 3.6 20.2 1.0
O A:GLY566 4.1 19.2 1.0
CA A:GLY565 4.1 18.8 1.0
N A:GLY566 4.6 17.7 1.0
O A:HOH1643 4.7 35.2 1.0
C A:GLY566 4.8 18.4 1.0
CA A:GLY566 4.9 17.1 1.0

Calcium binding site 9 out of 9 in 6f2p

Go back to Calcium Binding Sites List in 6f2p
Calcium binding site 9 out of 9 in the Structure of Paenibacillus Xanthan Lyase to 2.6 A Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Structure of Paenibacillus Xanthan Lyase to 2.6 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1109

b:46.0
occ:1.00
 OE1 A:GLN698 2.5 24.7 1.0
O A:HOH1347 2.7 33.1 1.0
O A:HOH1561 2.8 39.3 1.0
O A:HOH1661 2.9 31.7 1.0
O A:HOH1499 3.0 14.6 1.0
CD A:GLN698 3.6 17.9 1.0
O A:ALA206 3.9 27.2 1.0
NE2 A:GLN698 4.1 13.9 1.0
CA A:GLY741 4.1 17.3 1.0
O A:GLY741 4.4 19.1 1.0
C A:GLY741 4.5 17.8 1.0
CA A:GLY369 4.7 18.7 1.0
O A:SER368 4.7 17.3 1.0
CD A:ARG390 4.8 23.1 1.0
CE2 A:TYR212 4.9 19.6 1.0
CG A:GLN698 4.9 18.8 1.0
O A:HOH1417 4.9 25.9 1.0
O A:HOH1272 4.9 14.5 1.0

Reference:

P.F.Jensen, A.Kadziola, G.Comamala, D.R.Segura, L.Anderson, J.N.Poulsen, K.K.Rasmussen, S.Agarwal, R.K.Sainathan, R.N.Monrad, A.Svendsen, J.E.Nielsen, L.Lo Leggio, K.D.Rand. Structure and Dynamics of A Promiscuous Xanthan Lyase From Paenibacillus Nanensis and the Design of Variants with Increased Stability and Activity. Cell Chem Biol V. 26 191 2019.
ISSN: ESSN 2451-9448
PubMed: 30503284
DOI: 10.1016/J.CHEMBIOL.2018.10.016
Page generated: Mon Jul 15 18:43:29 2024

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