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Calcium in PDB 5j6y: Crystal Structure of PA14 Domain of Mpafp Antifreeze Protein

Protein crystallography data

The structure of Crystal Structure of PA14 Domain of Mpafp Antifreeze Protein, PDB code: 5j6y was solved by S.Guo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.71 / 1.03
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 45.220, 50.550, 79.420, 90.00, 90.00, 90.00
R / Rfree (%) 15.5 / 16.4

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of PA14 Domain of Mpafp Antifreeze Protein (pdb code 5j6y). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Crystal Structure of PA14 Domain of Mpafp Antifreeze Protein, PDB code: 5j6y:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 5j6y

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Calcium binding site 1 out of 8 in the Crystal Structure of PA14 Domain of Mpafp Antifreeze Protein


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of PA14 Domain of Mpafp Antifreeze Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca301

b:4.5
occ:1.00
 OD1 A:ASP155 2.3 4.3 1.0
OD1 A:ASP110 2.3 4.8 1.0
O A:ASP159 2.4 5.0 1.0
OD2 A:ASP111 2.4 4.4 1.0
O A:GLY157 2.4 5.1 1.0
O4 A:BGC310 2.5 20.0 0.2
O4 A:GLC309 2.5 5.2 0.8
O3 A:BGC310 2.5 20.0 0.2
O3 A:GLC309 2.5 5.5 0.8
CG A:ASP110 3.3 4.8 1.0
CG A:ASP111 3.3 4.4 1.0
C3 A:GLC309 3.4 6.6 0.8
C4 A:GLC309 3.4 6.3 0.8
C3 A:BGC310 3.4 20.0 0.2
C4 A:BGC310 3.4 20.0 0.2
C A:GLY157 3.4 4.5 1.0
CG A:ASP155 3.5 4.0 1.0
C A:ASP159 3.6 4.9 1.0
OD2 A:ASP110 3.6 6.0 1.0
OD1 A:ASP111 3.7 4.9 1.0
N A:ASP159 3.9 6.0 1.0
N A:GLY157 3.9 5.0 1.0
N A:GLN156 4.2 4.1 1.0
C A:GLY158 4.2 5.5 1.0
N A:GLY158 4.3 5.1 1.0
CA A:GLY157 4.3 5.2 1.0
CA A:ASP159 4.3 5.6 0.5
CA A:ASP159 4.3 5.8 0.5
OD2 A:ASP155 4.3 4.6 1.0
CB A:ASP155 4.4 4.1 1.0
CA A:ASP155 4.4 4.0 1.0
CA A:GLY158 4.4 6.0 1.0
N A:ASP111 4.5 4.2 1.0
C A:ASP110 4.5 4.1 1.0
CG A:GLN156 4.5 6.0 1.0
CB A:ASP111 4.5 4.5 1.0
NE2 A:GLN156 4.6 8.2 1.0
N A:TYR160 4.6 5.4 1.0
CB A:ASP110 4.6 5.3 1.0
O A:ASP110 4.7 4.2 1.0
C A:ASP155 4.7 4.5 1.0
C5 A:BGC310 4.7 20.0 0.2
C2 A:BGC310 4.7 20.0 0.2
C5 A:GLC309 4.7 7.9 0.8
C2 A:GLC309 4.7 8.8 0.8
CA A:TYR160 4.8 5.4 1.0
C A:GLN156 4.8 4.8 1.0
O A:GLY158 4.9 6.3 1.0
CA A:ASP111 4.9 4.3 1.0
O A:GLN129 4.9 6.7 1.0

Calcium binding site 2 out of 8 in 5j6y

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Calcium binding site 2 out of 8 in the Crystal Structure of PA14 Domain of Mpafp Antifreeze Protein


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of PA14 Domain of Mpafp Antifreeze Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca302

b:5.4
occ:1.00
 OE1 A:GLN27 2.3 6.3 1.0
O A:GLN156 2.3 5.5 1.0
O A:HOH609 2.4 6.8 1.0
O A:HOH628 2.4 6.7 1.0
OD1 A:ASP87 2.4 4.8 1.0
O A:HOH476 2.4 9.5 1.0
OD2 A:ASP87 2.5 4.9 1.0
CG A:ASP87 2.8 4.6 1.0
C A:GLN156 3.4 4.8 1.0
CD A:GLN27 3.5 6.3 1.0
CA A:GLN156 4.0 4.6 1.0
OE1 A:GLN156 4.0 8.3 1.0
CB A:GLN156 4.2 5.3 1.0
CA A:GLN27 4.2 5.3 1.0
NE2 A:GLN27 4.3 7.0 1.0
CB A:ASP87 4.3 4.7 1.0
CD A:GLN156 4.4 7.1 1.0
CB A:GLN27 4.4 5.8 1.0
O A:HOH482 4.4 6.9 1.0
O A:HOH456 4.5 8.4 1.0
OG1 A:THR86 4.5 5.1 1.0
O A:HOH680 4.5 32.6 1.0
N A:GLY157 4.6 5.0 1.0
CG A:GLN27 4.6 6.5 1.0
O A:SER26 4.7 6.6 1.0
N A:LEU28 4.7 5.0 1.0
O A:THR86 4.8 5.2 1.0
CA A:GLY157 4.9 5.2 1.0
CB A:THR86 4.9 5.1 1.0
CG A:GLN156 4.9 6.0 1.0
NE2 A:GLN156 4.9 8.2 1.0

Calcium binding site 3 out of 8 in 5j6y

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Calcium binding site 3 out of 8 in the Crystal Structure of PA14 Domain of Mpafp Antifreeze Protein


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of PA14 Domain of Mpafp Antifreeze Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca303

b:7.6
occ:0.53
 O A:SER73 2.3 10.4 1.0
O A:HOH630 2.4 21.0 1.0
O A:HOH645 2.5 17.5 1.0
O A:HOH552 2.5 12.3 1.0
OG A:SER76 2.6 7.9 1.0
O A:HOH550 2.6 12.2 1.0
O A:HOH526 2.6 18.3 1.0
C A:SER73 3.4 8.8 1.0
CB A:SER76 3.6 6.7 1.0
CA A:SER73 4.0 9.0 1.0
N A:SER76 4.4 5.1 1.0
N A:ASP74 4.5 6.2 1.0
CB A:SER73 4.6 9.8 1.0
CA A:SER76 4.6 5.5 1.0
CA A:ASP74 4.8 5.1 1.0
O A:HOH435 4.9 11.4 1.0
C A:ASP74 5.0 5.3 1.0

Calcium binding site 4 out of 8 in 5j6y

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Calcium binding site 4 out of 8 in the Crystal Structure of PA14 Domain of Mpafp Antifreeze Protein


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of PA14 Domain of Mpafp Antifreeze Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca304

b:4.9
occ:1.00
 O A:PRO82 2.3 5.2 1.0
O A:HOH444 2.4 8.3 1.0
O A:HOH527 2.4 6.2 1.0
O A:GLY64 2.4 5.7 1.0
O A:HOH538 2.4 6.0 1.0
OD1 A:ASP81 2.5 5.2 1.0
O A:HOH512 2.5 4.9 1.0
CG A:ASP81 3.5 4.9 1.0
C A:GLY64 3.5 5.2 1.0
C A:PRO82 3.5 5.8 1.0
OD2 A:ASP81 3.9 5.8 1.0
O A:HOH428 4.2 4.8 1.0
N A:PRO82 4.2 5.5 1.0
CA A:GLY64 4.2 5.6 1.0
O A:HOH685 4.3 27.7 1.0
CA A:PRO82 4.4 6.0 1.0
C A:ASP81 4.4 5.6 1.0
OE1 A:GLN68 4.4 5.1 1.0
O A:GLY83 4.4 5.1 1.0
N A:GLY64 4.4 5.3 1.0
N A:GLY83 4.5 5.7 1.0
C A:GLY83 4.5 4.9 1.0
CD A:PRO82 4.5 5.8 1.0
N A:THR65 4.5 5.2 1.0
CA A:GLY83 4.5 5.8 1.0
NE2 A:GLN68 4.6 5.6 1.0
O A:ASP81 4.7 6.6 1.0
CA A:THR65 4.8 5.0 1.0
O A:HOH679 4.8 13.5 1.0
CB A:ASP81 4.8 5.4 1.0
CB A:PRO82 4.8 8.7 1.0
O A:HOH626 4.8 31.8 1.0
OD1 A:ASP84 4.8 6.9 1.0
O A:HOH480 4.8 26.2 1.0
CA A:ASP81 4.9 5.3 1.0
C A:LYS63 5.0 4.7 0.6
CD A:GLN68 5.0 4.5 1.0

Calcium binding site 5 out of 8 in 5j6y

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Calcium binding site 5 out of 8 in the Crystal Structure of PA14 Domain of Mpafp Antifreeze Protein


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of PA14 Domain of Mpafp Antifreeze Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca305

b:13.9
occ:0.49
 OD1 A:ASP7 2.3 29.9 1.0
OE1 A:GLN5 2.4 23.0 1.0
O A:THR9 2.4 20.2 1.0
O A:HOH414 2.4 28.7 1.0
O A:HOH408 2.4 35.1 1.0
OD1 A:ASP11 2.5 19.4 1.0
OD2 A:ASP11 2.5 23.4 1.0
CG A:ASP11 2.8 21.7 1.0
CG A:ASP7 3.3 42.2 1.0
CD A:GLN5 3.4 21.5 1.0
C A:THR9 3.5 19.2 1.0
OD2 A:ASP7 3.6 38.8 1.0
NE2 A:GLN5 3.7 22.1 1.0
CB A:THR9 4.0 28.1 1.0
CA A:THR9 4.1 27.6 1.0
N A:THR9 4.1 25.7 1.0
CB A:ASP11 4.3 16.6 1.0
N A:ASP7 4.5 34.3 1.0
N A:ASP11 4.5 16.0 1.0
OD1 A:ASP6 4.5 57.6 1.0
C A:PRO10 4.6 16.7 1.0
CB A:ASP7 4.6 36.3 1.0
N A:PRO10 4.6 17.3 1.0
CG2 A:THR9 4.7 33.2 1.0
CG A:GLN5 4.8 25.6 1.0
N A:ASP6 4.8 51.1 1.0
CA A:ASP11 4.8 12.9 1.0
C A:ASP7 4.8 34.2 1.0
CA A:ASP7 4.8 39.4 1.0
CA A:PRO10 4.9 16.1 1.0
O A:ASP7 4.9 29.8 1.0
O A:PRO10 5.0 19.4 1.0

Calcium binding site 6 out of 8 in 5j6y

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Calcium binding site 6 out of 8 in the Crystal Structure of PA14 Domain of Mpafp Antifreeze Protein


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of PA14 Domain of Mpafp Antifreeze Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca306

b:13.6
occ:0.50
 O A:HOH627 2.4 24.6 1.0
O A:HOH640 2.4 29.4 1.0
O A:VAL38 2.4 9.4 1.0
O A:LYS41 2.5 9.0 1.0
O A:HOH625 2.5 21.6 1.0
OH A:TYR22 2.6 10.1 1.0
CZ A:TYR22 3.5 7.1 1.0
C A:VAL38 3.6 8.2 1.0
C A:LYS41 3.6 8.7 1.0
CE2 A:TYR22 3.7 7.8 1.0
O A:HOH590 3.8 23.2 1.0
CG1 A:VAL38 4.2 8.6 1.0
CA A:GLU42 4.3 10.3 1.0
O A:HOH555 4.3 17.9 1.0
N A:GLU42 4.4 9.5 1.0
CA A:VAL38 4.5 7.0 1.0
N A:LYS41 4.5 8.5 1.0
CA A:ASP39 4.5 9.5 0.5
N A:ASP39 4.5 7.8 1.0
C A:GLU42 4.6 8.2 1.0
N A:ALA43 4.6 8.0 1.0
OE1 A:GLU20 4.7 10.8 1.0
CA A:LYS41 4.7 9.0 1.0
O A:HOH633 4.7 32.4 1.0
CA A:ASP39 4.7 8.7 0.5
C A:ASP39 4.7 9.4 1.0
CE1 A:TYR22 4.7 7.0 1.0
OE2 A:GLU42 4.8 37.6 1.0
O A:ASP39 5.0 12.2 1.0
CD2 A:TYR22 5.0 6.4 1.0
CB A:VAL38 5.0 7.4 1.0

Calcium binding site 7 out of 8 in 5j6y

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Calcium binding site 7 out of 8 in the Crystal Structure of PA14 Domain of Mpafp Antifreeze Protein


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of PA14 Domain of Mpafp Antifreeze Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca307

b:5.8
occ:0.53
 O A:HOH472 2.4 11.4 1.0
O A:HOH681 2.4 15.9 1.0
O A:HOH653 2.4 15.6 1.0
O A:HOH576 2.4 10.6 1.0
O A:HOH534 2.5 10.1 1.0
O A:HOH610 2.7 15.4 1.0
O A:SER53 4.1 5.3 1.0
CA A:GLY72 4.4 7.3 1.0
O A:GLY55 4.5 8.2 1.0
O A:HOH567 4.5 10.8 1.0
O A:HOH461 4.5 16.7 1.0
O A:HOH638 4.6 20.8 1.0
O A:PHE70 4.7 4.9 1.0
O A:GLU69 4.8 5.5 1.0
O A:HOH648 4.8 39.6 1.0
N A:GLY72 4.9 6.8 1.0

Calcium binding site 8 out of 8 in 5j6y

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Calcium binding site 8 out of 8 in the Crystal Structure of PA14 Domain of Mpafp Antifreeze Protein


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of PA14 Domain of Mpafp Antifreeze Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca308

b:21.4
occ:0.37
 O A:SER172 2.3 7.7 0.5
O A:HOH522 2.4 33.3 1.0
O A:SER172 2.6 8.7 0.5
O A:HOH508 2.6 24.4 1.0
O A:HOH659 2.6 21.5 1.0
C A:SER172 3.5 7.7 0.5
O A:HOH545 3.6 29.8 1.0
C A:SER172 3.6 9.3 0.5
CA A:SER172 4.4 7.9 0.5
N A:THR173 4.5 8.1 1.0
CA A:SER172 4.5 9.5 0.5
CA A:THR173 4.5 7.9 1.0
O A:GLY171 4.7 11.4 1.0

Reference:

S.Guo, C.A.Stevens, T.D.R.Vance, L.L.C.Olijve, L.A.Graham, R.L.Campbell, S.R.Yazdi, C.Escobedo, M.Bar-Dolev, V.Yashunsky, I.Braslavsky, D.N.Langelaan, S.P.Smith, J.S.Allingham, I.K.Voets, P.L.Davies. Structure of A 1.5-Mda Adhesin That Binds Its Antarctic Bacterium to Diatoms and Ice. Sci Adv V. 3 01440 2017.
ISSN: ESSN 2375-2548
PubMed: 28808685
DOI: 10.1126/SCIADV.1701440
Page generated: Sun Jul 14 20:53:13 2024

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