Atomistry » Calcium » PDB 5ekk-5eyh » 5eq4
Atomistry »
  Calcium »
    PDB 5ekk-5eyh »
      5eq4 »

Calcium in PDB 5eq4: Crystal Structure of the Srpa Adhesin R347E Mutant From Streptococcus Sanguinis

Protein crystallography data

The structure of Crystal Structure of the Srpa Adhesin R347E Mutant From Streptococcus Sanguinis, PDB code: 5eq4 was solved by L.V.Loukachevitch, K.M.Mcculloch, K.R.Vann, Z.Wawrzak, S.Anderson, T.M.Iverson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.35 / 2.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 44.700, 88.055, 199.214, 90.00, 90.00, 90.00
R / Rfree (%) 20.2 / 25.7

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of the Srpa Adhesin R347E Mutant From Streptococcus Sanguinis (pdb code 5eq4). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 9 binding sites of Calcium where determined in the Crystal Structure of the Srpa Adhesin R347E Mutant From Streptococcus Sanguinis, PDB code: 5eq4:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Calcium binding site 1 out of 9 in 5eq4

Go back to Calcium Binding Sites List in 5eq4
Calcium binding site 1 out of 9 in the Crystal Structure of the Srpa Adhesin R347E Mutant From Streptococcus Sanguinis


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 the Srpa Adhesin R347E Mutant From Streptococcus Sanguinis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca501

b:30.9
occ:1.00
OD2 A:ASP353 2.4 30.7 1.0
OD1 A:ASP282 2.4 27.4 1.0
OD2 A:ASP281 2.4 29.8 1.0
OD1 A:ASP253 2.4 33.1 1.0
O A:THR255 2.4 32.4 1.0
OD1 A:ASP281 2.4 29.0 1.0
OD2 A:ASP253 2.4 29.1 1.0
CG A:ASP281 2.7 31.3 1.0
CG A:ASP253 2.8 33.4 1.0
CG A:ASP282 3.5 32.2 1.0
CG A:ASP353 3.5 34.3 1.0
C A:THR255 3.6 35.7 1.0
OD2 A:ASP282 3.9 41.3 1.0
CB A:ASP353 4.0 34.6 1.0
N A:THR255 4.2 35.9 1.0
CB A:THR255 4.2 38.4 1.0
CA A:THR255 4.2 39.6 1.0
CB A:ASP281 4.3 26.9 1.0
CB A:ASP253 4.3 33.0 1.0
N A:ASP282 4.3 26.6 1.0
N A:SER283 4.3 25.7 1.0
O A:HOH671 4.4 37.1 1.0
OG A:SER283 4.4 29.8 1.0
ND2 A:ASN357 4.4 34.4 1.0
CB A:SER283 4.5 36.1 1.0
OD1 A:ASP353 4.5 35.0 1.0
N A:PRO256 4.6 35.2 1.0
C A:PRO256 4.7 30.3 1.0
CB A:ASP282 4.8 27.3 1.0
CA A:PRO256 4.8 36.5 1.0
O A:PRO256 4.9 32.1 1.0
CG2 A:THR255 4.9 33.0 1.0
CA A:ASP281 4.9 28.7 1.0
CA A:ASP282 5.0 26.4 1.0
C A:ASP281 5.0 27.5 1.0

Calcium binding site 2 out of 9 in 5eq4

Go back to Calcium Binding Sites List in 5eq4
Calcium binding site 2 out of 9 in the Crystal Structure of the Srpa Adhesin R347E Mutant From Streptococcus Sanguinis


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 the Srpa Adhesin R347E Mutant From Streptococcus Sanguinis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca502

b:28.5
occ:1.00
OD2 A:ASP434 2.3 17.2 1.0
O A:THR372 2.3 22.9 1.0
O A:TYR375 2.4 29.2 1.0
OD1 A:ASP434 2.4 22.0 1.0
OG1 A:THR372 2.5 22.4 1.0
O A:HOH707 2.5 35.9 1.0
CG A:ASP434 2.7 19.7 1.0
O A:HOH719 3.2 32.2 1.0
O A:HOH602 3.2 40.9 1.0
C A:THR372 3.3 21.5 1.0
CB A:THR372 3.6 18.6 1.0
C A:TYR375 3.6 22.4 1.0
CA A:THR372 3.6 20.6 1.0
CB A:ASP434 4.2 18.8 1.0
OH A:TYR428 4.3 19.9 1.0
N A:ASN376 4.5 22.7 1.0
CA A:ASN376 4.5 27.0 1.0
OD1 A:ASN376 4.5 44.7 1.0
N A:ASP373 4.5 24.9 1.0
CG2 A:THR372 4.5 20.0 1.0
CD A:PRO377 4.6 28.7 1.0
CA A:TYR375 4.6 24.8 1.0
N A:TYR375 4.6 24.6 1.0
CE2 A:TYR428 4.7 13.0 1.0
O A:THR433 4.9 17.1 1.0
CZ A:TYR428 4.9 17.0 1.0
CB A:TYR375 5.0 20.6 1.0
CA A:ASP373 5.0 23.1 1.0

Calcium binding site 3 out of 9 in 5eq4

Go back to Calcium Binding Sites List in 5eq4
Calcium binding site 3 out of 9 in the Crystal Structure of the Srpa Adhesin R347E Mutant From Streptococcus Sanguinis


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 the Srpa Adhesin R347E Mutant From Streptococcus Sanguinis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca503

b:25.5
occ:1.00
OE2 A:GLU400 2.4 19.1 1.0
OE2 B:GLU400 2.4 19.3 1.0
OE1 A:GLU400 2.5 18.5 1.0
OE1 B:GLU400 2.5 17.5 1.0
O B:HOH647 2.7 26.6 1.0
O A:HOH633 2.7 9.5 1.0
CD A:GLU400 2.8 16.1 1.0
CD B:GLU400 2.8 18.2 1.0
O A:HOH678 2.8 23.0 1.0
O B:HOH609 2.8 15.7 1.0
O B:HOH662 4.2 16.8 1.0
O A:HOH650 4.2 14.9 1.0
CG A:GLU400 4.3 16.2 1.0
CG B:GLU400 4.3 11.7 1.0
NH2 B:ARG415 4.3 14.0 1.0
NH1 B:ARG415 4.3 13.4 1.0
NH1 A:ARG415 4.4 13.0 1.0
NH2 A:ARG415 4.5 12.1 1.0
O A:HOH681 4.5 13.5 1.0
O B:ILE416 4.6 12.6 1.0
CZ B:ARG415 4.6 16.9 1.0
O A:ILE416 4.7 17.1 1.0
CZ A:ARG415 4.8 14.5 1.0
O B:HOH687 5.0 16.4 1.0

Calcium binding site 4 out of 9 in 5eq4

Go back to Calcium Binding Sites List in 5eq4
Calcium binding site 4 out of 9 in the Crystal Structure of the Srpa Adhesin R347E Mutant From Streptococcus Sanguinis


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 the Srpa Adhesin R347E Mutant From Streptococcus Sanguinis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca501

b:67.9
occ:1.00
ND2 B:ASN357 2.3 60.5 1.0
OD1 B:ASP253 2.4 59.5 1.0
OD2 B:ASP253 2.4 60.0 1.0
O B:THR255 2.4 51.5 1.0
OD2 B:ASP353 2.4 50.4 1.0
OD1 B:ASP281 2.4 57.0 1.0
OD2 B:ASP281 2.5 55.1 1.0
OD2 B:ASP282 2.6 65.6 1.0
CG B:ASP253 2.6 57.5 1.0
CG B:ASP281 2.8 57.5 1.0
CG B:ASP353 3.6 52.2 1.0
CG B:ASN357 3.6 60.1 1.0
C B:THR255 3.6 57.9 1.0
CG B:ASP282 3.8 62.8 1.0
CB B:ASP253 4.0 60.9 1.0
CB B:ASP353 4.1 50.5 1.0
CB B:ASN357 4.3 52.7 1.0
CB B:ASP281 4.3 55.2 1.0
N B:THR255 4.3 63.2 1.0
C B:PRO256 4.4 54.7 1.0
N B:ASP282 4.5 64.2 1.0
CA B:PRO256 4.5 54.5 1.0
OD1 B:ASN357 4.5 55.5 1.0
N B:PRO256 4.5 56.0 1.0
CA B:THR255 4.5 66.5 1.0
OD1 B:ASP353 4.6 46.7 1.0
N B:PRO257 4.6 53.5 1.0
CG2 B:THR255 4.6 62.3 1.0
OD1 B:ASP282 4.6 68.9 1.0
O B:PRO256 4.6 51.3 1.0
CD B:PRO257 4.7 48.1 1.0
CB B:ASP282 4.7 63.7 1.0
CA B:ASP253 4.9 55.4 1.0
C B:ASP253 4.9 53.5 1.0
N B:THR254 5.0 55.4 1.0
CG B:PRO257 5.0 47.0 1.0

Calcium binding site 5 out of 9 in 5eq4

Go back to Calcium Binding Sites List in 5eq4
Calcium binding site 5 out of 9 in the Crystal Structure of the Srpa Adhesin R347E Mutant From Streptococcus Sanguinis


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 the Srpa Adhesin R347E Mutant From Streptococcus Sanguinis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca502

b:35.4
occ:1.00
O B:THR372 2.3 22.7 1.0
O B:TYR375 2.3 30.2 1.0
OD2 B:ASP434 2.3 19.9 1.0
OD1 B:ASP434 2.4 20.8 1.0
OG1 B:THR372 2.4 21.1 1.0
O B:HOH708 2.5 30.2 1.0
CG B:ASP434 2.7 21.6 1.0
C B:THR372 3.3 22.1 1.0
C B:TYR375 3.5 25.3 1.0
CB B:THR372 3.6 19.9 1.0
CA B:THR372 3.7 18.4 1.0
O B:HOH664 3.9 55.5 1.0
CB B:ASP434 4.2 20.8 1.0
OH B:TYR428 4.3 21.5 1.0
CA B:TYR375 4.3 27.4 1.0
N B:TYR375 4.4 24.9 1.0
N B:ASP373 4.4 21.5 1.0
CG2 B:THR372 4.5 16.0 1.0
N B:ASN376 4.5 24.2 1.0
CB B:TYR375 4.5 20.6 1.0
CD B:PRO377 4.5 24.9 1.0
CE2 B:TYR428 4.7 18.3 1.0
CA B:ASN376 4.7 27.7 1.0
CA B:ASP373 4.8 23.9 1.0
CZ B:TYR428 4.8 16.3 1.0
CA B:ASP434 4.9 18.7 1.0
O B:THR433 4.9 19.8 1.0

Calcium binding site 6 out of 9 in 5eq4

Go back to Calcium Binding Sites List in 5eq4
Calcium binding site 6 out of 9 in the Crystal Structure of the Srpa Adhesin R347E Mutant From Streptococcus Sanguinis


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 the Srpa Adhesin R347E Mutant From Streptococcus Sanguinis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca501

b:47.3
occ:1.00
OD2 C:ASP253 2.3 55.4 1.0
OD1 C:ASP282 2.3 49.2 1.0
O C:THR255 2.4 43.2 1.0
OD2 C:ASP353 2.4 43.3 1.0
OD2 C:ASP281 2.4 39.5 1.0
OD1 C:ASP281 2.4 41.7 1.0
OD1 C:ASP253 2.5 46.9 1.0
CG C:ASP253 2.7 52.6 1.0
CG C:ASP281 2.7 42.0 1.0
CG C:ASP353 3.4 44.1 1.0
CG C:ASP282 3.4 48.2 1.0
C C:THR255 3.6 42.8 1.0
CB C:ASP353 3.8 40.2 1.0
OD2 C:ASP282 3.9 56.0 1.0
OG C:SER283 4.1 46.0 1.0
ND2 C:ASN357 4.1 39.9 1.0
CB C:ASP253 4.1 48.8 1.0
CB C:ASP281 4.2 42.2 1.0
N C:THR255 4.2 43.9 1.0
N C:ASP282 4.3 41.4 1.0
CA C:THR255 4.3 44.5 1.0
CB C:THR255 4.4 45.7 1.0
N C:SER283 4.4 43.9 1.0
OD1 C:ASP353 4.4 43.4 1.0
N C:PRO256 4.6 43.1 1.0
C C:PRO256 4.6 40.4 1.0
CB C:SER283 4.7 44.9 1.0
CB C:ASP282 4.7 38.1 1.0
CA C:PRO256 4.7 42.3 1.0
N C:PRO257 4.9 45.4 1.0
CA C:ASP281 4.9 40.8 1.0
O C:PRO256 4.9 41.4 1.0
CA C:ASP282 4.9 42.2 1.0
C C:ASP281 5.0 42.5 1.0
CG C:ASN357 5.0 45.7 1.0

Calcium binding site 7 out of 9 in 5eq4

Go back to Calcium Binding Sites List in 5eq4
Calcium binding site 7 out of 9 in the Crystal Structure of the Srpa Adhesin R347E Mutant From Streptococcus Sanguinis


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 the Srpa Adhesin R347E Mutant From Streptococcus Sanguinis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca502

b:28.1
occ:1.00
O C:TYR375 2.3 20.3 1.0
O C:THR372 2.3 20.1 1.0
OD2 C:ASP434 2.3 13.5 1.0
OD1 C:ASP434 2.4 17.3 1.0
OG1 C:THR372 2.4 16.1 1.0
CG C:ASP434 2.7 13.4 1.0
O C:HOH691 3.3 21.9 1.0
C C:THR372 3.3 18.0 1.0
C C:TYR375 3.6 19.9 1.0
CB C:THR372 3.6 15.8 1.0
CA C:THR372 3.8 15.9 1.0
O C:HOH627 4.2 31.9 1.0
CB C:ASP434 4.2 12.2 1.0
OD1 C:ASN376 4.3 22.4 1.0
OH C:TYR428 4.3 13.0 1.0
N C:ASP373 4.4 18.2 1.0
N C:TYR375 4.4 20.6 1.0
CA C:TYR375 4.4 17.6 1.0
CD C:PRO377 4.5 17.9 1.0
CG2 C:THR372 4.5 16.0 1.0
N C:ASN376 4.5 20.4 1.0
CA C:ASN376 4.6 22.0 1.0
CB C:TYR375 4.7 18.6 1.0
CA C:ASP373 4.8 24.1 1.0
CE2 C:TYR428 4.8 17.1 1.0
O C:THR433 4.8 14.2 1.0
CZ C:TYR428 4.9 15.4 1.0
CA C:ASP434 5.0 13.3 1.0

Calcium binding site 8 out of 9 in 5eq4

Go back to Calcium Binding Sites List in 5eq4
Calcium binding site 8 out of 9 in the Crystal Structure of the Srpa Adhesin R347E Mutant From Streptococcus Sanguinis


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 the Srpa Adhesin R347E Mutant From Streptococcus Sanguinis within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca501

b:35.2
occ:1.00
OD2 D:ASP353 2.3 39.0 1.0
OD1 D:ASP281 2.4 32.2 1.0
OD2 D:ASP253 2.4 40.8 1.0
OD1 D:ASP253 2.4 40.4 1.0
OD2 D:ASP281 2.4 33.4 1.0
O D:THR255 2.5 35.9 1.0
CG D:ASP353 2.5 31.9 1.0
OD1 D:ASP282 2.6 39.2 1.0
CG D:ASP253 2.7 40.0 1.0
CG D:ASP281 2.7 29.0 1.0
CB D:ASP353 3.1 34.3 1.0
OD1 D:ASP353 3.1 35.4 1.0
CG D:ASP282 3.7 37.9 1.0
C D:THR255 3.8 33.5 1.0
OG D:SER283 4.1 34.3 1.0
O D:HOH639 4.1 33.1 1.0
OD2 D:ASP282 4.2 41.9 1.0
OG1 D:THR255 4.2 39.7 1.0
CB D:ASP253 4.2 42.2 1.0
CB D:ASP281 4.2 30.0 1.0
ND2 D:ASN357 4.3 32.6 1.0
C D:PRO256 4.5 29.0 1.0
CA D:PRO256 4.5 32.6 1.0
N D:SER283 4.5 27.7 1.0
N D:ASP282 4.6 31.2 1.0
N D:PRO256 4.6 36.9 1.0
CA D:ASP353 4.6 33.0 1.0
CB D:SER283 4.6 33.9 1.0
N D:THR255 4.6 35.4 1.0
N D:PRO257 4.7 33.9 1.0
O D:HOH679 4.7 33.8 1.0
CA D:THR255 4.7 34.3 1.0
O D:PRO256 4.8 31.2 1.0
CD D:PRO257 4.8 31.0 1.0
CB D:ASN357 4.9 33.0 1.0

Calcium binding site 9 out of 9 in 5eq4

Go back to Calcium Binding Sites List in 5eq4
Calcium binding site 9 out of 9 in the Crystal Structure of the Srpa Adhesin R347E Mutant From Streptococcus Sanguinis


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 the Srpa Adhesin R347E Mutant From Streptococcus Sanguinis within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca502

b:31.7
occ:1.00
O D:THR372 2.3 17.3 1.0
O D:TYR375 2.3 17.4 1.0
OD2 D:ASP434 2.3 20.1 1.0
OD1 D:ASP434 2.4 19.8 1.0
OG1 D:THR372 2.4 19.8 1.0
CG D:ASP434 2.7 19.7 1.0
O D:HOH736 2.8 25.3 1.0
C D:THR372 3.2 17.6 1.0
O D:HOH702 3.5 28.6 1.0
C D:TYR375 3.5 19.4 1.0
CB D:THR372 3.5 16.8 1.0
CA D:THR372 3.6 18.6 1.0
O D:HOH724 4.1 24.7 1.0
CB D:ASP434 4.2 20.6 1.0
CD D:PRO377 4.2 21.6 1.0
OH D:TYR428 4.3 15.2 1.0
CA D:TYR375 4.3 19.8 1.0
N D:TYR375 4.3 16.4 1.0
CB D:TYR375 4.4 16.5 1.0
N D:ASP373 4.4 20.0 1.0
CG2 D:THR372 4.5 15.8 1.0
N D:ASN376 4.5 18.4 1.0
OD1 D:ASN376 4.6 25.3 1.0
CE2 D:TYR428 4.6 18.5 1.0
O D:THR433 4.7 14.6 1.0
CA D:ASN376 4.7 21.4 1.0
CZ D:TYR428 4.9 13.8 1.0
CA D:ASP434 4.9 16.0 1.0
CA D:ASP373 4.9 21.4 1.0
CG D:PRO377 5.0 18.8 1.0

Reference:

B.A.Bensing, L.V.Loukachevitch, K.M.Mcculloch, H.Yu, K.R.Vann, Z.Wawrzak, S.Anderson, X.Chen, P.M.Sullam, T.M.Iverson. Structural Basis For Sialoglycan Binding By the Streptococcus Sanguinis Srpa Adhesin. J.Biol.Chem. V. 291 7230 2016.
ISSN: ESSN 1083-351X
PubMed: 26833566
DOI: 10.1074/JBC.M115.701425
Page generated: Sun Jul 14 18:41:52 2024

Last articles

Ca in 3DE6
Ca in 3DE5
Ca in 3DE4
Ca in 3DE3
Ca in 3DE2
Ca in 3DE1
Ca in 3DD4
Ca in 3DE0
Ca in 3DDZ
Ca in 3DBZ
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy