Calcium in PDB 5k8g: Crystal Structure of A Putative Peptide-Binding Domain of Mpafp

The structure of Crystal Structure of A Putative Peptide-Binding Domain of Mpafp, PDB code: 5k8g was solved by S.Guo, R.Campbell, P.Davies, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.64 / 2.00
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	50.115, 61.065, 63.473, 66.25, 72.66, 67.94
R / Rfree (%)	18.3 / 22.1

Pages:

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

Binding sites:

The binding sites of Calcium atom in the Crystal Structure of A Putative Peptide-Binding Domain of Mpafp (pdb code 5k8g). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 16 binding sites of Calcium where determined in the Crystal Structure of A Putative Peptide-Binding Domain of Mpafp, PDB code: 5k8g:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 16 in the Crystal Structure of A Putative Peptide-Binding Domain of Mpafp


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 A Putative Peptide-Binding Domain of Mpafp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca601 b:47.7 occ:1.00 O A:HOH750 2.2 47.2 1.0 O A:HOH858 2.2 40.6 1.0 O A:HOH913 2.3 53.3 1.0 O A:GLU79 2.4 41.4 1.0 OD1 A:ASP77 2.4 46.9 1.0 O A:HOH953 2.5 49.4 1.0 OD2 A:ASP77 2.5 46.1 1.0 CG A:ASP77 2.8 48.4 1.0 C A:GLU79 3.6 41.7 1.0 CB A:ASP77 4.3 42.4 1.0 O A:HOH834 4.3 48.6 1.0 CA A:PHE80 4.3 39.6 1.0 N A:PHE80 4.4 37.9 1.0 CB A:PHE80 4.4 44.2 1.0 CA A:GLU79 4.6 46.2 1.0 O A:HOH931 4.6 41.2 1.0 N A:GLU79 4.6 43.0 1.0 O A:THR48 4.7 39.7 1.0 CB A:GLU79 4.8 51.6 1.0 O A:HOH981 4.9 52.8 1.0 CG A:GLU79 5.0 66.9 1.0

Calcium binding site 2 out of 16 in the Crystal Structure of A Putative Peptide-Binding Domain of Mpafp


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 A Putative Peptide-Binding Domain of Mpafp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca602 b:40.4 occ:1.00 O A:HOH928 2.3 34.5 1.0 O A:THR101 2.3 38.2 1.0 O A:HOH975 2.3 34.5 1.0 O A:HOH923 2.4 44.1 1.0 O A:HOH835 2.4 36.2 1.0 OD2 A:ASP17 2.5 44.1 1.0 OD1 A:ASP17 2.8 42.6 1.0 CG A:ASP17 3.0 41.7 1.0 C A:THR101 3.5 38.9 1.0 N A:THR101 4.1 41.7 1.0 CA A:CA610 4.1 68.2 1.0 OG1 A:THR101 4.2 41.1 1.0 OG A:SER100 4.3 41.2 1.0 CA A:THR101 4.4 42.4 1.0 CB A:ASP17 4.4 41.3 1.0 N A:HIS102 4.5 36.6 1.0 CA A:HIS102 4.5 37.8 1.0 O A:HOH828 4.6 41.5 1.0 CA A:ALA12 4.6 39.6 1.0 CB A:HIS102 4.7 37.5 1.0 N A:ILE13 4.9 36.6 1.0 CG1 A:ILE13 4.9 36.4 1.0 O A:HOH936 4.9 56.8 1.0 O A:ASN11 4.9 39.1 1.0

Calcium binding site 3 out of 16 in the Crystal Structure of A Putative Peptide-Binding Domain of Mpafp


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 A Putative Peptide-Binding Domain of Mpafp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca603 b:28.4 occ:1.00 OE2 A:GLU116 2.4 32.6 1.0 OD1 A:ASP191 2.4 30.3 1.0 OD2 A:ASP492 2.4 28.6 1.0 OD1 A:ASP426 2.4 28.2 1.0 O A:ARG161 2.5 28.5 1.0 OE1 A:GLU116 2.6 33.5 1.0 OD2 A:ASP426 2.6 30.0 1.0 ND1 A:HIS163 2.7 31.7 1.0 CD A:GLU116 2.8 32.4 1.0 CG A:ASP426 2.9 32.2 1.0 CG A:ASP492 3.4 30.7 1.0 CE1 A:HIS163 3.5 30.5 1.0 CG A:ASP191 3.5 33.3 1.0 C A:ARG161 3.6 33.1 1.0 OD1 A:ASP492 3.7 25.5 1.0 CG A:HIS163 3.7 31.4 1.0 CA A:CA604 3.9 30.5 1.0 CB A:HIS163 4.0 27.8 1.0 N A:HIS163 4.0 31.7 1.0 N A:ARG161 4.2 32.4 1.0 CA A:ASP191 4.3 32.0 1.0 CB A:ASP191 4.3 32.2 1.0 O A:HOH742 4.3 30.2 1.0 CG A:GLU116 4.3 31.9 1.0 N A:SER192 4.3 29.5 1.0 CB A:ASP426 4.4 35.7 1.0 OD2 A:ASP191 4.4 38.3 1.0 CA A:ARG161 4.4 30.9 1.0 N A:ASP162 4.6 31.6 1.0 NE2 A:HIS163 4.7 33.4 1.0 CA A:HIS163 4.7 33.1 1.0 CA A:ASP162 4.7 34.9 1.0 CB A:ASP492 4.7 30.5 1.0 OG A:SER192 4.8 35.2 1.0 CB A:ARG161 4.8 33.8 1.0 CD2 A:HIS163 4.8 32.1 1.0 C A:ASP162 4.8 32.6 1.0 CG1 A:VAL160 4.8 34.9 1.0 C A:ASP191 4.9 29.8 1.0 O A:SER192 4.9 29.1 1.0

Calcium binding site 4 out of 16 in the Crystal Structure of A Putative Peptide-Binding Domain of Mpafp


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 A Putative Peptide-Binding Domain of Mpafp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca604 b:30.5 occ:1.00 OD1 A:ASP492 2.2 25.5 1.0 OD2 A:ASP426 2.3 30.0 1.0 O A:SER192 2.3 29.1 1.0 OG A:SER494 2.3 28.8 1.0 OD2 A:ASP490 2.5 31.2 1.0 OD1 A:ASP191 2.5 30.3 1.0 OD2 A:ASP191 2.7 38.3 1.0 CG A:ASP191 2.9 33.3 1.0 OD1 A:ASP490 3.0 29.1 1.0 CG A:ASP490 3.1 32.4 1.0 CG A:ASP492 3.3 30.7 1.0 CB A:SER494 3.4 28.6 1.0 CG A:ASP426 3.5 32.2 1.0 C A:SER192 3.5 29.4 1.0 OD2 A:ASP492 3.7 28.6 1.0 CA A:CA603 3.9 28.4 1.0 O A:HOH792 4.1 43.4 1.0 N A:SER192 4.2 29.5 1.0 CB A:ASP426 4.2 35.7 1.0 N A:SER494 4.2 31.7 1.0 OE2 A:GLU116 4.3 32.6 1.0 CB A:ASP191 4.4 32.2 1.0 OD1 A:ASP426 4.4 28.2 1.0 CA A:SER494 4.4 28.1 1.0 N A:ALA193 4.4 29.2 1.0 CA A:SER192 4.5 32.3 1.0 CA A:ALA193 4.5 33.7 1.0 OG A:SER192 4.6 35.2 1.0 CB A:ASP490 4.6 35.8 1.0 CB A:ASP492 4.7 30.5 1.0 O A:HOH727 4.8 43.9 1.0 C A:ASP191 4.8 29.8 1.0 N A:ASP492 4.8 34.9 1.0 C A:ASP492 4.9 28.7 1.0 CA A:ASP191 5.0 32.0 1.0 CA A:ASP492 5.0 32.2 1.0

Calcium binding site 5 out of 16 in the Crystal Structure of A Putative Peptide-Binding Domain of Mpafp


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 A Putative Peptide-Binding Domain of Mpafp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca605 b:30.8 occ:1.00 O A:VAL167 2.3 33.9 1.0 O A:ASP162 2.3 32.0 1.0 O A:HOH797 2.4 25.4 1.0 OD1 A:ASP165 2.4 30.2 1.0 O A:HOH768 2.4 27.2 1.0 OD1 A:ASP169 2.5 35.8 1.0 OD2 A:ASP169 2.5 36.9 1.0 CG A:ASP169 2.9 32.4 1.0 CG A:ASP165 3.3 34.2 1.0 C A:VAL167 3.5 32.8 1.0 C A:ASP162 3.5 32.6 1.0 OD2 A:ASP165 3.7 36.2 1.0 N A:VAL167 4.2 36.8 1.0 CA A:VAL167 4.2 34.8 1.0 CA A:HIS163 4.2 33.1 1.0 N A:HIS163 4.2 31.7 1.0 CB A:ASP169 4.3 31.7 1.0 CB A:VAL167 4.3 37.1 1.0 O A:HOH740 4.4 51.5 1.0 O A:ASP165 4.4 29.2 1.0 C A:SER168 4.4 31.2 1.0 N A:ASP165 4.4 34.1 1.0 O A:SER168 4.5 26.3 1.0 CA A:ASP162 4.5 34.9 1.0 N A:SER168 4.5 36.6 1.0 N A:ASP169 4.5 32.2 1.0 C A:HIS163 4.6 35.0 1.0 CB A:ASP165 4.6 35.6 1.0 C A:ASP165 4.6 30.5 1.0 N A:ASP162 4.6 31.6 1.0 CA A:ASP165 4.7 32.5 1.0 NH2 A:ARG161 4.7 32.0 1.0 CB A:ASP162 4.8 35.3 1.0 O A:HOH901 4.8 27.8 1.0 CA A:SER168 4.8 35.4 1.0 CA A:ASP169 4.8 31.3 1.0 NE A:ARG161 4.9 28.6 1.0 O A:HIS163 4.9 36.0 1.0 N A:GLY164 4.9 37.7 1.0 CG1 A:VAL167 4.9 39.9 1.0 CB A:ARG161 5.0 33.8 1.0

Calcium binding site 6 out of 16 in the Crystal Structure of A Putative Peptide-Binding Domain of Mpafp


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 A Putative Peptide-Binding Domain of Mpafp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca606 b:32.4 occ:1.00 O A:VAL197 2.3 34.8 1.0 O A:ILE412 2.3 34.5 1.0 OD1 A:ASP421 2.4 29.1 1.0 OD1 A:ASP199 2.4 34.3 1.0 OH A:TYR486 2.5 26.7 1.0 O A:HOH707 2.5 31.4 1.0 OD2 A:ASP199 2.6 39.5 1.0 CG A:ASP199 2.8 36.4 1.0 CG A:ASP421 3.3 31.4 1.0 C A:ILE412 3.5 32.0 1.0 C A:VAL197 3.5 36.1 1.0 OD2 A:ASP421 3.5 32.2 1.0 CZ A:TYR486 3.7 27.8 1.0 N A:VAL197 4.0 33.3 1.0 CB A:ILE412 4.1 30.8 1.0 CA A:ILE412 4.1 33.0 1.0 CA A:VAL197 4.2 34.3 1.0 CE1 A:TYR486 4.3 28.6 1.0 CB A:ASP199 4.3 36.2 1.0 O A:ASP414 4.4 39.3 1.0 CB A:VAL197 4.4 35.3 1.0 C A:ASP198 4.4 36.7 1.0 O A:ASP198 4.5 33.8 1.0 CB A:ASP421 4.6 35.9 1.0 N A:ASP198 4.6 34.6 1.0 N A:ASP421 4.6 37.4 1.0 N A:PHE413 4.6 36.2 1.0 N A:ASP199 4.7 34.5 1.0 CE2 A:TYR486 4.8 28.9 1.0 OD1 A:ASN416 4.8 46.2 1.0 O A:HOH811 4.8 35.5 1.0 CA A:PHE413 4.9 39.1 1.0 O A:GLY419 4.9 38.5 1.0 CA A:ASP198 4.9 35.4 1.0 CA A:ASP199 4.9 35.7 1.0 CA A:ASP421 4.9 34.7 1.0 CG2 A:ILE412 4.9 32.5 1.0

Calcium binding site 7 out of 16 in the Crystal Structure of A Putative Peptide-Binding Domain of Mpafp


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 A Putative Peptide-Binding Domain of Mpafp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca607 b:29.2 occ:1.00 OD1 A:ASN290 2.3 33.0 1.0 OE1 A:GLU330 2.4 30.8 1.0 O A:TYR291 2.4 35.1 1.0 OD2 A:ASP342 2.4 31.4 1.0 OE1 A:GLU385 2.6 29.0 1.0 OE2 A:GLU385 2.7 31.5 1.0 CD A:GLU385 3.0 33.5 1.0 CD A:GLU330 3.3 31.2 1.0 CG A:ASN290 3.4 26.5 1.0 CG A:ASP342 3.4 29.1 1.0 C A:TYR291 3.5 32.9 1.0 CG A:GLU330 3.7 30.7 1.0 OD1 A:ASP342 3.8 26.0 1.0 ND2 A:ASN290 3.8 26.9 1.0 CA A:CA608 3.9 31.8 1.0 OG A:SER260 4.0 27.4 1.0 O A:HOH806 4.1 31.6 1.0 CA A:PRO292 4.2 34.2 1.0 N A:PRO292 4.2 35.9 1.0 N A:TYR291 4.2 28.9 1.0 OE2 A:GLU330 4.3 32.1 1.0 CA A:TYR291 4.5 29.8 1.0 CG A:GLU385 4.5 35.7 1.0 N A:VAL293 4.6 30.1 1.0 ND2 A:ASN333 4.6 34.8 1.0 C A:ASN290 4.6 28.3 1.0 CB A:ASN290 4.7 25.7 1.0 OD1 A:ASN333 4.7 34.8 1.0 CB A:ASP342 4.7 28.5 1.0 C A:PRO292 4.8 30.8 1.0 CA A:ASN290 4.9 27.6 1.0

Calcium binding site 8 out of 16 in the Crystal Structure of A Putative Peptide-Binding Domain of Mpafp


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 A Putative Peptide-Binding Domain of Mpafp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca608 b:31.8 occ:1.00 OD1 A:ASP342 2.3 26.0 1.0 O A:THR331 2.3 36.1 1.0 OD1 A:ASN333 2.4 34.8 1.0 OE2 A:GLU385 2.4 31.5 1.0 O A:SER340 2.4 29.7 1.0 OG1 A:THR331 2.6 34.0 1.0 C A:THR331 3.3 33.5 1.0 CD A:GLU385 3.3 33.5 1.0 CG A:ASP342 3.3 29.1 1.0 N A:THR331 3.4 33.1 1.0 C A:SER340 3.5 31.5 1.0 CG A:ASN333 3.6 36.2 1.0 CA A:THR331 3.6 32.5 1.0 CB A:THR331 3.7 34.2 1.0 OD2 A:ASP342 3.8 31.4 1.0 CA A:CA607 3.9 29.2 1.0 CG A:GLU385 4.1 35.7 1.0 OE1 A:GLU385 4.1 29.0 1.0 ND2 A:ASN333 4.2 34.8 1.0 CA A:SER340 4.2 33.5 1.0 O A:ARG341 4.2 29.2 1.0 C A:ARG341 4.3 32.2 1.0 C A:GLU330 4.3 34.4 1.0 C A:PRO332 4.4 37.9 1.0 O A:PRO332 4.5 43.1 1.0 N A:PRO332 4.5 35.6 1.0 N A:ASP342 4.5 29.1 1.0 N A:ASN333 4.5 36.5 1.0 N A:ARG341 4.5 34.2 1.0 CB A:ASP342 4.6 28.5 1.0 CB A:SER340 4.7 32.1 1.0 CA A:ASN333 4.7 38.1 1.0 CB A:ASN333 4.7 38.1 1.0 ND2 A:ASN290 4.7 26.9 1.0 CA A:ASP342 4.7 29.4 1.0 CA A:ARG341 4.8 34.0 1.0 CG2 A:THR331 4.9 34.5 1.0 CA A:PRO332 4.9 41.2 1.0 CA A:GLU330 4.9 34.3 1.0

Calcium binding site 9 out of 16 in the Crystal Structure of A Putative Peptide-Binding Domain of Mpafp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Crystal Structure of A Putative Peptide-Binding Domain of Mpafp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca609 b:36.9 occ:1.00 O A:THR18 2.2 35.5 1.0 O A:HOH801 2.2 45.6 1.0 OE2 A:GLU23 2.3 40.7 1.0 O A:HOH773 2.4 38.6 1.0 OE1 A:GLU23 2.4 39.4 1.0 OG1 A:THR14 2.4 38.7 1.0 OD1 A:ASP16 2.5 48.0 1.0 CD A:GLU23 2.8 36.0 1.0 CB A:THR14 3.3 41.1 1.0 C A:THR18 3.4 38.2 1.0 CG A:ASP16 3.4 48.5 1.0 OD2 A:ASP16 3.7 50.5 1.0 CG2 A:THR14 3.9 39.8 1.0 N A:THR18 4.1 37.0 1.0 CG A:GLU23 4.3 36.3 1.0 CA A:THR18 4.3 39.8 1.0 N A:ILE19 4.3 34.1 1.0 OD2 A:ASP20 4.4 56.3 1.0 CA A:ILE19 4.4 36.8 1.0 O A:ILE13 4.5 39.5 1.0 N A:ASP20 4.6 36.8 1.0 CA A:THR14 4.7 40.4 1.0 CG A:ASP20 4.7 44.7 1.0 N A:ASP16 4.8 46.0 1.0 CB A:ASP16 4.8 50.9 1.0 C A:THR14 4.9 41.7 1.0 C A:ILE19 4.9 38.9 1.0 N A:ASP17 5.0 38.5 1.0

Calcium binding site 10 out of 16 in the Crystal Structure of A Putative Peptide-Binding Domain of Mpafp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Crystal Structure of A Putative Peptide-Binding Domain of Mpafp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca610 b:68.2 occ:1.00 OD2 A:ASP17 2.6 44.1 1.0 O A:HOH712 2.6 47.0 1.0 O A:HOH1004 2.7 59.1 1.0 O A:HOH1026 2.7 52.6 1.0 O A:HOH974 2.7 55.1 1.0 O A:HOH936 2.7 56.8 1.0 O A:HOH923 2.8 44.1 1.0 CG A:ASP17 3.8 41.7 1.0 CA A:CA602 4.1 40.4 1.0 CB A:ASP17 4.3 41.3 1.0 OG1 A:THR101 4.5 41.1 1.0 O A:THR101 4.5 38.2 1.0 O A:ASP17 4.8 36.5 1.0 OD1 A:ASP17 4.8 42.6 1.0 OG A:SER103 4.8 43.5 1.0 CA A:HIS102 4.8 37.8 1.0 O A:HOH975 5.0 34.5 1.0

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