Sodium in PDB 3gxw: Structure of the SH2 Domain of the Candida Glabrata Transcription Elongation Factor SPT6, Crystal Form A

Protein crystallography data

The structure of Structure of the SH2 Domain of the Candida Glabrata Transcription Elongation Factor SPT6, Crystal Form A, PDB code: 3gxw was solved by S.Dengl, A.Mayer, M.Sun, P.Cramer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	20.00 / 1.90
*Space group*	P 6₅
*Cell size a, b, c (Å), α, β, γ (°)*	54.499, 54.499, 253.434, 90.00, 90.00, 120.00
*R / R_free (%)*	19.6 / 24.1

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of the SH2 Domain of the Candida Glabrata Transcription Elongation Factor SPT6, Crystal Form A (pdb code 3gxw). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Structure of the SH2 Domain of the Candida Glabrata Transcription Elongation Factor SPT6, Crystal Form A, PDB code: 3gxw:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 3gxw

Go back to

Sodium Binding Sites List in 3gxw

Sodium binding site 1 out of 4 in the Structure of the SH2 Domain of the Candida Glabrata Transcription Elongation Factor SPT6, Crystal Form A

Mono view

Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of the SH2 Domain of the Candida Glabrata Transcription Elongation Factor SPT6, Crystal Form A within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Na104 b:28.4 occ:1.00	O	A:SER38	2.5	13.9	1.0
	O	A:HOH1027	2.6	29.3	1.0
	O	A:HOH105	2.6	18.0	1.0
	O	A:HOH115	2.6	22.1	1.0
	O	A:GLY41	2.7	15.4	1.0
	C	A:GLY41	3.4	18.0	1.0
	C	A:SER38	3.5	17.1	1.0
	CA	A:ASP42	4.0	21.4	1.0
	N	A:ASP42	4.0	19.6	1.0
	N	A:SER38	4.0	15.4	1.0
	OE1	A:GLN37	4.2	24.1	1.0
	N	A:GLY41	4.3	19.3	1.0
	CA	A:SER38	4.3	17.8	1.0
	N	A:SER39	4.3	16.9	1.0
	CA	A:GLY41	4.4	18.8	1.0
	O	A:HIS44	4.4	16.0	1.0
	OD1	A:ASP42	4.4	31.5	1.0
	CA	A:SER39	4.5	17.3	1.0
	C	A:ASP42	4.6	20.4	1.0
	O	A:ASP42	4.8	20.6	1.0
	C	A:SER39	4.9	18.2	1.0

Sodium binding site 2 out of 4 in 3gxw

Go back to

Sodium Binding Sites List in 3gxw

Sodium binding site 2 out of 4 in the Structure of the SH2 Domain of the Candida Glabrata Transcription Elongation Factor SPT6, Crystal Form A

Mono view

Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of the SH2 Domain of the Candida Glabrata Transcription Elongation Factor SPT6, Crystal Form A within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
B:Na104 b:25.3 occ:1.00	O	B:SER38	2.6	19.7	1.0
	O	B:HOH112	2.7	21.3	1.0
	O	B:HOH1286	2.7	27.7	1.0
	O	B:GLY41	2.7	19.6	1.0
	C	B:GLY41	3.4	22.5	1.0
	C	B:SER38	3.6	18.1	1.0
	N	B:ASP42	4.1	24.6	1.0
	N	B:SER38	4.2	15.8	1.0
	CA	B:ASP42	4.2	27.9	1.0
	N	B:GLY41	4.2	17.4	1.0
	CA	B:GLY41	4.3	20.0	1.0
	N	B:SER39	4.4	16.1	1.0
	CA	B:SER39	4.4	18.4	1.0
	OE1	B:GLN37	4.5	20.0	1.0
	O	B:HIS44	4.5	15.8	1.0
	CA	B:SER38	4.5	16.7	1.0
	OD1	B:ASP42	4.5	34.4	1.0
	C	B:ASP42	4.9	28.0	1.0
	C	B:SER39	4.9	17.4	1.0

Sodium binding site 3 out of 4 in 3gxw

Go back to

Sodium Binding Sites List in 3gxw

Sodium binding site 3 out of 4 in the Structure of the SH2 Domain of the Candida Glabrata Transcription Elongation Factor SPT6, Crystal Form A

Mono view

Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of the SH2 Domain of the Candida Glabrata Transcription Elongation Factor SPT6, Crystal Form A within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
C:Na104 b:30.0 occ:1.00	O	C:SER38	2.6	19.7	1.0
	O	C:HOH1112	2.7	20.4	1.0
	O	C:HOH1018	2.7	29.7	1.0
	O	C:HOH1031	2.7	35.2	1.0
	O	C:GLY41	2.7	18.7	1.0
	C	C:GLY41	3.4	19.4	1.0
	C	C:SER38	3.6	19.3	1.0
	N	C:ASP42	4.0	20.5	1.0
	N	C:SER38	4.0	18.6	1.0
	CA	C:ASP42	4.1	25.1	1.0
	N	C:GLY41	4.1	18.2	1.0
	OD1	C:ASP42	4.2	29.6	1.0
	CA	C:GLY41	4.2	18.8	1.0
	O	C:HOH1449	4.2	40.4	1.0
	CA	C:SER38	4.4	19.8	1.0
	O	C:HIS44	4.5	18.4	1.0
	OE1	C:GLN37	4.5	32.5	1.0
	N	C:SER39	4.6	18.4	1.0
	CA	C:SER39	4.7	18.7	1.0
	C	C:ASP42	4.9	25.3	1.0
	CB	C:GLN37	4.9	24.1	1.0
	C	C:SER39	5.0	18.1	1.0

Sodium binding site 4 out of 4 in 3gxw

Go back to

Sodium Binding Sites List in 3gxw

Sodium binding site 4 out of 4 in the Structure of the SH2 Domain of the Candida Glabrata Transcription Elongation Factor SPT6, Crystal Form A

Mono view

Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structure of the SH2 Domain of the Candida Glabrata Transcription Elongation Factor SPT6, Crystal Form A within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
D:Na104 b:31.3 occ:1.00	O	D:SER38	2.5	14.5	1.0
	O	D:HOH105	2.6	15.7	1.0
	O	D:HOH117	2.7	24.0	1.0
	O	D:GLY41	2.7	16.6	1.0
	O	D:HOH1022	2.7	32.4	1.0
	O	D:HOH136	2.7	30.1	1.0
	C	D:GLY41	3.4	17.1	1.0
	C	D:SER38	3.6	17.0	1.0
	N	D:SER38	4.0	18.0	1.0
	N	D:ASP42	4.0	16.8	1.0
	CA	D:ASP42	4.1	20.1	1.0
	CE	D:MSE4	4.2	70.7	1.0
	N	D:GLY41	4.2	16.7	1.0
	CA	D:GLY41	4.3	16.2	1.0
	O	D:HOH1376	4.3	35.3	1.0
	CA	D:SER38	4.4	17.2	1.0
	O	D:HIS44	4.4	19.1	1.0
	OD1	D:ASP42	4.5	26.0	1.0
	N	D:SER39	4.5	17.2	1.0
	OE1	D:GLN37	4.5	29.5	1.0
	CA	D:SER39	4.6	17.3	1.0
	C	D:ASP42	4.7	20.2	1.0
	C	D:SER39	5.0	17.4	1.0

Reference:

S.Dengl, A.Mayer, M.Sun, P.Cramer. Structure and in Vivo Requirement of the Yeast SPT6 SH2 Domain J.Mol.Biol. V. 389 211 2009.
ISSN: ISSN 0022-2836
PubMed: 19371747
DOI: 10.1016/J.JMB.2009.04.016

Page generated: Mon Oct 7 10:18:34 2024

Last articles

F in 4H3J
F in 4GXJ
F in 4GVH
F in 4GU9
F in 4GSI
F in 4GPT
F in 4GTO
F in 4GS9
F in 4GQ4
F in 4GPB

	© Copyright 2008-2020 by atomistry.com
Home \| Site Map \| Copyright \| Contact us \| Privacy