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Calcium in PDB 8vdk: Crystal Structure of Lpxtg-Motif Cell Wall Anchor Domain Protein MSCRAMM_SDRD From Staphylococcus Aureus

Protein crystallography data

The structure of Crystal Structure of Lpxtg-Motif Cell Wall Anchor Domain Protein MSCRAMM_SDRD From Staphylococcus Aureus, PDB code: 8vdk was solved by Y.Kim, A.Tan, M.Endres, A.Joachimiak, Center For Structural Biology Ofinfectious Diseases (Csbid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.33 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 43.054, 72.825, 148.453, 90, 90, 90
R / Rfree (%) 17.9 / 21.1

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Lpxtg-Motif Cell Wall Anchor Domain Protein MSCRAMM_SDRD From Staphylococcus Aureus (pdb code 8vdk). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Crystal Structure of Lpxtg-Motif Cell Wall Anchor Domain Protein MSCRAMM_SDRD From Staphylococcus Aureus, PDB code: 8vdk:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 8vdk

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Calcium binding site 1 out of 5 in the Crystal Structure of Lpxtg-Motif Cell Wall Anchor Domain Protein MSCRAMM_SDRD From Staphylococcus Aureus


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 Lpxtg-Motif Cell Wall Anchor Domain Protein MSCRAMM_SDRD From Staphylococcus Aureus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca512

b:31.3
occ:0.71
 O A:VAL44 2.2 23.7 1.0
O A:HOH865 2.3 27.8 1.0
O A:ASP42 2.4 23.5 1.0
O A:HOH633 2.4 32.4 1.0
O A:HOH861 2.5 38.7 1.0
O A:VAL103 2.5 22.9 1.0
C A:ASP42 3.3 26.5 1.0
C A:VAL44 3.4 27.6 1.0
C A:VAL103 3.6 26.5 1.0
N A:VAL44 3.9 23.0 1.0
CA A:ASP42 3.9 24.2 1.0
CB A:VAL103 3.9 23.4 1.0
CA A:VAL44 4.1 23.7 1.0
O A:ASP41 4.2 20.5 1.0
CA A:VAL103 4.2 25.4 1.0
C A:LYS43 4.2 26.6 1.0
O A:HOH660 4.3 46.6 1.0
N A:LYS43 4.3 25.1 1.0
O A:PHE106 4.4 23.1 1.0
N A:LYS45 4.5 25.7 1.0
CG2 A:VAL103 4.6 22.7 1.0
CB A:VAL44 4.6 22.6 1.0
CA A:LYS45 4.7 23.9 1.0
N A:ASP104 4.7 22.4 1.0
CA A:LYS43 4.7 24.2 1.0
O A:LYS43 4.7 28.1 1.0
OD1 A:ASN107 4.8 27.9 1.0
O A:HOH669 4.8 23.0 1.0
CB A:ASP42 4.8 28.2 1.0
N A:ASP42 5.0 23.2 1.0

Calcium binding site 2 out of 5 in 8vdk

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Calcium binding site 2 out of 5 in the Crystal Structure of Lpxtg-Motif Cell Wall Anchor Domain Protein MSCRAMM_SDRD From Staphylococcus Aureus


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 Lpxtg-Motif Cell Wall Anchor Domain Protein MSCRAMM_SDRD From Staphylococcus Aureus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca513

b:21.4
occ:1.00
 OD1 A:ASP336 2.3 24.1 1.0
OE1 A:GLU344 2.3 22.9 1.0
O A:VAL342 2.4 23.7 1.0
OE2 A:GLU347 2.4 26.3 1.0
OD1 A:ASN338 2.5 27.0 1.0
OD1 A:ASN340 2.5 22.6 1.0
OE1 A:GLU347 2.6 24.5 1.0
CD A:GLU347 2.9 25.5 1.0
CG A:ASN338 3.4 26.9 1.0
CD A:GLU344 3.4 30.1 1.0
CG A:ASP336 3.5 22.2 1.0
CG A:ASN340 3.5 24.6 1.0
C A:VAL342 3.6 23.7 1.0
ND2 A:ASN338 3.7 30.0 1.0
CG A:GLU344 3.9 26.2 1.0
ND2 A:ASN340 4.0 24.5 1.0
N A:VAL342 4.0 21.5 1.0
OD2 A:ASP336 4.1 22.0 1.0
CA A:VAL342 4.3 23.6 1.0
CB A:GLU344 4.3 25.5 1.0
CG A:GLU347 4.4 22.9 1.0
NE1 A:TRP334 4.5 22.1 1.0
OE2 A:GLU344 4.5 34.3 1.0
N A:ASN340 4.5 21.9 1.0
N A:GLU344 4.5 20.6 1.0
CB A:ASP336 4.6 20.8 1.0
N A:GLN343 4.6 19.5 1.0
CA A:ASP336 4.6 23.8 1.0
N A:ASN338 4.6 25.9 1.0
CB A:VAL342 4.7 22.4 1.0
CB A:ASN340 4.7 21.9 1.0
O A:HOH663 4.7 29.9 1.0
N A:GLY341 4.7 20.8 1.0
CB A:ASN338 4.8 24.9 1.0
C A:ASP336 4.8 23.7 1.0
CA A:GLN343 4.8 19.8 1.0
C A:GLN343 4.9 21.0 1.0
N A:THR337 4.9 22.7 1.0
N A:LYS339 4.9 22.2 1.0
CA A:ASN340 5.0 22.1 1.0

Calcium binding site 3 out of 5 in 8vdk

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Calcium binding site 3 out of 5 in the Crystal Structure of Lpxtg-Motif Cell Wall Anchor Domain Protein MSCRAMM_SDRD From Staphylococcus Aureus


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 Lpxtg-Motif Cell Wall Anchor Domain Protein MSCRAMM_SDRD From Staphylococcus Aureus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca514

b:20.3
occ:1.00
 O A:GLU409 2.3 20.0 1.0
OD1 A:ASN414 2.4 20.6 1.0
O A:SER429 2.4 19.2 1.0
OD1 A:ASP412 2.4 20.6 1.0
O A:HOH678 2.4 21.1 1.0
O A:HOH742 2.4 20.8 1.0
O A:HOH694 2.5 19.7 1.0
C A:GLU409 3.4 20.6 1.0
CG A:ASN414 3.4 18.5 1.0
CG A:ASP412 3.5 21.0 1.0
C A:SER429 3.6 19.9 1.0
ND2 A:ASN414 3.8 19.6 1.0
OD2 A:ASP412 3.9 21.8 1.0
CA A:GLU409 3.9 20.0 1.0
CB A:SER429 4.0 22.6 1.0
OG A:SER429 4.2 21.7 1.0
CB A:GLU409 4.2 21.8 1.0
CA A:SER429 4.3 19.9 1.0
O A:ASP412 4.4 21.4 1.0
N A:GLU410 4.5 20.0 1.0
N A:ASP431 4.6 20.7 1.0
O A:HOH879 4.6 26.6 1.0
N A:ALA430 4.6 20.3 1.0
C A:ASP412 4.7 20.3 1.0
CB A:ASN414 4.7 18.8 1.0
O A:HOH743 4.7 27.3 1.0
N A:ASN414 4.7 19.5 1.0
CA A:GLU410 4.8 21.1 1.0
N A:ASP412 4.8 19.7 1.0
CA A:ALA430 4.8 19.4 1.0
OD2 A:ASP431 4.8 20.7 1.0
CB A:ASP412 4.8 18.6 1.0
CA A:ASN414 4.9 19.1 1.0
C A:SER413 5.0 19.5 1.0

Calcium binding site 4 out of 5 in 8vdk

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Calcium binding site 4 out of 5 in the Crystal Structure of Lpxtg-Motif Cell Wall Anchor Domain Protein MSCRAMM_SDRD From Staphylococcus Aureus


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 Lpxtg-Motif Cell Wall Anchor Domain Protein MSCRAMM_SDRD From Staphylococcus Aureus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca515

b:29.1
occ:1.00
 OD1 A:ASP18 2.3 25.9 1.0
OD1 A:ASP20 2.3 28.9 1.0
O A:THR24 2.4 29.2 1.0
O A:HOH712 2.5 28.8 1.0
OG A:SER22 2.5 29.6 1.0
OD1 A:ASP30 2.6 28.1 1.0
OD2 A:ASP30 2.6 28.0 1.0
CG A:ASP30 2.9 26.8 1.0
CG A:ASP20 3.4 37.5 1.0
CG A:ASP18 3.5 24.5 1.0
CB A:SER22 3.6 29.8 1.0
C A:THR24 3.6 31.2 1.0
OD2 A:ASP20 3.7 31.8 1.0
N A:SER22 4.0 29.1 1.0
OG1 A:THR24 4.2 33.2 1.0
OD2 A:ASP18 4.2 28.6 1.0
CA A:ASP18 4.3 22.7 1.0
CA A:SER22 4.3 30.1 1.0
N A:THR24 4.4 28.0 1.0
CB A:ASP18 4.4 23.8 1.0
CA A:ILE25 4.4 28.7 1.0
CB A:ASP30 4.4 25.6 1.0
N A:ILE25 4.4 28.3 1.0
N A:ASP20 4.5 24.9 1.0
C A:ASP18 4.5 26.9 1.0
CA A:THR24 4.5 28.5 1.0
N A:ALA19 4.6 22.5 1.0
N A:VAL26 4.6 26.4 1.0
CB A:GLN29 4.6 31.4 1.0
CD1 A:ILE25 4.7 31.9 1.0
CB A:ASP20 4.7 35.2 1.0
N A:ASN21 4.8 28.2 1.0
N A:LYS23 4.9 31.4 1.0
C A:SER22 4.9 31.2 1.0
O A:HOH847 4.9 43.3 1.0
CA A:ASP20 4.9 30.6 1.0
C A:ASP20 5.0 28.7 1.0
C A:ILE25 5.0 29.7 1.0

Calcium binding site 5 out of 5 in 8vdk

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Calcium binding site 5 out of 5 in the Crystal Structure of Lpxtg-Motif Cell Wall Anchor Domain Protein MSCRAMM_SDRD From Staphylococcus Aureus


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 Lpxtg-Motif Cell Wall Anchor Domain Protein MSCRAMM_SDRD From Staphylococcus Aureus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca516

b:20.1
occ:1.00
 O A:LEU428 2.3 20.3 1.0
OD1 A:ASN331 2.3 22.7 1.0
O A:HOH708 2.4 18.6 1.0
O2 A:EDO511 2.4 21.8 1.0
OD2 A:ASP431 2.4 20.7 1.0
OD1 A:ASP431 2.5 20.4 1.0
O A:HOH601 2.5 53.8 1.0
O1 A:EDO511 2.5 21.7 1.0
CG A:ASP431 2.8 21.9 1.0
C2 A:EDO511 3.3 31.2 1.0
CG A:ASN331 3.4 23.1 1.0
C1 A:EDO511 3.4 34.4 1.0
C A:LEU428 3.5 21.7 1.0
N A:ASN331 4.0 21.7 1.0
ND2 A:ASN331 4.1 19.8 1.0
CA A:SER429 4.1 19.9 1.0
CB A:TYR332 4.2 19.0 1.0
O A:HOH643 4.2 22.2 1.0
N A:SER429 4.2 19.5 1.0
O A:GLU410 4.3 21.5 1.0
CB A:ASP431 4.3 17.3 1.0
OE2 A:GLU81 4.3 23.4 1.0
CB A:LEU428 4.4 19.8 1.0
CB A:ASN331 4.5 19.0 1.0
CA A:LEU428 4.5 21.5 1.0
C A:SER429 4.6 19.9 1.0
N A:TYR332 4.6 22.0 1.0
CA A:ASN331 4.6 21.5 1.0
C A:ASN331 4.7 23.5 1.0
NE2 A:GLN343 4.7 19.5 1.0
O A:GLY330 4.7 21.7 1.0
C A:GLY330 4.7 20.6 1.0
OE1 A:GLN343 4.8 20.6 1.0
O A:HOH678 4.9 21.1 1.0
N A:ALA430 4.9 20.3 1.0

Reference:

Y.Kim, A.Tan, M.Endres, A.Joachimiak, Center For Structural Biology Of Infectious Diseases (Csbid). Crystal Structure of Lpxtg-Motif Cell Wall Anchor Domain Protein MSCRAMM_SDRD From Staphylococcus Aureus To Be Published.
Page generated: Sat Sep 28 09:15:32 2024

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